arXiv subjects

Rastko Sknepnek

Publications and source records attributed to Rastko Sknepnek.

At least 19 recordsLinked to original sources

arXiv2026

Persistence-Driven Void Formation in Dense Active-Passive Mixtures

It is well established that dilute active dopants can melt an arrested amorphous solid by enhancing cage breaking and accelerating structural relaxation. Yet it remains unclear whether increasing persistence simply amplifies this effective melting or instead reorganizes the fluidization mechanism itself. Here we show that, in a minimal active-passive mixture, increasing persistence drives a crossover from homogeneous fluidization to a localized mechanical instability, demonstrating that sustained active forcing restructures relaxation in space rather than merely strengthening it. Persistent dopants accumulate stress and nucleate voids as their mechanically perturbed regions overlap. In this regime, rearrangements localize at void boundaries, and active and passive particles exhibit comparable mobility, producing dynamics reminiscent of crowd mosh pits. Persistence therefore reorganizes fluidization through stress accumulation and confinement, revealing a distinct nonequilibrium localization mechanism in disordered solids.

cond-mat.soft↗

arXiv2026

Emergent Dynamics of Active Systems on Curved Environments

Curvature plays a central role in the proper function of many biological processes. With active matter being a standard framework for understanding many aspects of the physics of life, it is natural to ask what effect curvature has on the collective behaviour of active matter. In this paper, we use the classical theory of surfaces to explore the active motion of self-propelled agents confined to move on a smooth curved two-dimensional surface embedded in Euclidean space. Even without interactions and alignment, the motion is non-trivially affected by the presence of curvature, leading to effects akin, e.g.\ to gravitational lensing and tidal forces. Such effects can lead to intermittent trapping of particles and profoundly affect their flocking behaviour. We show that these effects are governed by a geometric torque that, in the absence of noise and interactions, compels particles to move along geodesics.

cond-mat.soft↗

arXiv2026

Machine learning short-ranged many-body interactions in colloidal systems using descriptors based on Voronoi cells

Machine learning (ML) strategies are opening the door to faster computer simulations, allowing us to simulate more realistic colloidal systems. Since the interactions in colloidal systems are often highly many-body, stemming from e.g. depletion and steric interactions, one of the challenges for these algorithms is capturing the many-body nature of these interactions. In this paper, we introduce a new ML-based strategy for fitting many-body interactions in colloidal systems where the many-body interaction is highly local. To this end, we develop Voronoi-based descriptors for capturing the local environment and fit the effective potential using a simple neural network. To test this algorithm, we consider a simple two-dimensional model for a colloid-polymer mixture, where the colloid-colloid interactions and colloid-polymer interactions are hard-disk like, while the polymers themselves interact as ideal gas particles. We find that a Voronoi-based description is sufficient to accurately capture the many-body nature of this system. Moreover, we find that the Pearson correlation function alone is insufficient to determine the predictive power of the network emphasizing the importance of additional metrics when assessing the quality of ML-based potentials.

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.

cond-mat.soft↗

arXiv2025

Active Filaments on Curved Surfaces: From Single Filaments to Dilute Suspensions

Curvature plays a central organizational role in active polymer dynamics. Using large-scale Langevin-dynamics simulations, we study active semiflexible filaments confined to smooth curved surfaces and map how curvature, bending rigidity, and activity interact. We find geodesic alignment, curvature lensing, and curvature-induced trapping. In particular, regions of negative Gaussian curvature localize filaments and hinder global surface exploration. These results show how surface geometry can be used to control the organization and transport of active matter on curved substrates

cond-mat.soft↗

arXiv2025

Cell-level modelling of homeostasis in confined epithelial monolayers

Tissue homeostasis, the biological process of maintaining a steady state in tissue via control of cell proliferation, death, and metabolic function, is essential for the development, growth, maintenance, and proper function of living organisms. Disruptions to this process can lead to serious diseases and even death. In this study, we use the vertex model for the cell-level description of tissue mechanics to investigate the impact of the tissue microenvironment and local mechanical properties of cells on homeostasis in confined epithelial tissues. We find a dynamic steady state, where the balance between cell divisions and removals sustains homeostasis. By characterising homeostasis in terms of cell count, tissue area, and the cells' neighbour count distribution, we identify the factors that govern regulated and ordered tissue growth. This work, therefore, sheds light on the mechanisms underlying tissue homeostasis and highlights the importance of mechanics in the control of biological processes such as tissue development and disease pathology.

physics.bio-ph↗

arXiv2024

Vertex model with internal dissipation enables sustained flows

Complex tissue flows in epithelia are driven by intra- and inter-cellular processes that generate, maintain, and coordinate mechanical forces. There has been growing evidence that cell shape anisotropy, manifested as nematic order, plays an important role in this process. Here we extend an active nematic vertex model by replacing substrate friction with internal viscous dissipation, dominant in epithelia not supported by a substrate or the extracellular matrix, which are found in many early-stage embryos. When coupled to cell shape anisotropy, the internal viscous dissipation allows for long-range velocity correlations and thus enables the spontaneous emergence of flows with a large degree of spatiotemporal organisation. We demonstrate sustained flow in epithelial sheets confined to a channel, providing a link between the cell-level vertex model of tissue dynamics and continuum active nematics, whose behaviour in a channel is theoretically understood and experimentally realisable. Our findings also show a simple mechanism that could account for collective cell migration correlated over distances large compared to the cell size, as observed during morphogenesis.

cond-mat.soft↗

arXiv2023

PyMembrane: A flexible framework for efficient simulations of elastic and liquid membranes

PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is written in C++, with a flexible and intuitive Python interface, allowing for a quick setup, execution and analysis of complex simulations. PyMembrane follows modern software engineering principles and features a modular design that allows for straightforward implementation of custom extensions while ensuring consistency and enabling inexpensive maintenance. A hallmark feature of this design is the use of a standardized C++ interface which streamlines adding new functionalities. Furthermore, PyMembrane uses data structures optimised for unstructured meshes, ensuring efficient mesh operations and force calculations. By providing several templates for typical simulations supplemented by extensive documentation, the users can seamlessly set up and run research-level simulations and extend the package to integrate additional features, underscoring PyMembrane's commitment to user-centric design.

cond-mat.soft↗

arXiv2022

Shape-tension coupling produces nematic order in an epithelium vertex model

We study the vertex model for epithelial tissue mechanics extended to include coupling between the cell shapes and tensions in cell-cell junctions. This coupling represents an active force which drives the system out of equilibrium and leads to the formation of nematic order interspersed with prominent, long-lived $+1$ defects. The defects in the nematic ordering are coupled to the shape of the cell tiling, affecting cell areas and coordinations. This intricate interplay between cell shape, size, and coordination provides a possible mechanism by which tissues could spontaneously develop long-range polarity through local mechanical forces without resorting to long-range chemical patterning.

cond-mat.soft↗

arXiv2022

Linear Viscoelastic Response of the Vertex Model with Internal and External Dissipation: Normal Modes Analysis

We use the normal mode formalism to study the shear rheology of the vertex model for epithelial tissue mechanics in the overdamped linear response regime. We consider systems with external (e.g., cell-substrate) and internal (e.g., cell-cell) dissipation mechanisms, and derive expressions for stresses on cells due to mechanical and dissipative forces. The semi-analytical method developed here is, however, general and can be directly applied to study the linear response of a broad class of soft matter systems with internal and external dissipation. It involves normal mode decomposition to calculate linear loss and storage moduli of the system. Specifically, displacements along each normal mode produce stresses due to elastic deformation and internal dissipation, which are in force balance with loads due to external dissipation. Each normal mode responds with a characteristic relaxation timescale, and its rheological behavior can be described as a combination of a standard linear solid element due to elastic stresses and a Jeffreys model element due to the internal dissipative stresses. The total response of the system is then fully determined by connecting in parallel all the viscoelastic elements corresponding to individual normal modes. This allows full characterization of the potentially complex linear rheological response of the system at all driving frequencies and identification of collective excitations. We show that internal and external dissipation mechanisms lead to qualitatively different rheological behaviors due to the presence or absence of Jeffreys elements, which is particularly pronounced at high driving frequencies. Our findings, therefore, underscore the importance of microscopic dissipation mechanisms in understanding the rheological behavior of soft materials and tissues, in particular.

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↗

arXiv2022

Linear Viscoelastic Properties of the Vertex Model for Epithelial Tissues

Epithelial tissues act as barriers and, therefore, must repair themselves, respond to environmental changes and grow without compromising their integrity. Consequently, they exhibit complex viscoelastic rheological behavior where constituent cells actively tune their mechanical properties to change the overall response of the tissue, e.g., from solid-like to fluid-like. Mesoscopic mechanical properties of epithelia are commonly modeled with the vertex model. While previous studies have predominantly focused on the rheological properties of the vertex model at long time scales, we systematically studied the full dynamic range by applying small oscillatory shear and bulk deformations in both solid-like and fluid-like phases for regular hexagonal and disordered cell configurations. We found that the shear and bulk responses in the fluid and solid phases can be described by standard spring-dashpot viscoelastic models. Furthermore, the solid-fluid transition can be tuned by applying pre-deformation to the system. Our study provides insights into the mechanisms by which epithelia can regulate their rich rheological behavior.

cond-mat.soft↗

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

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↗

arXiv2019

Wrinkle patterns in active viscoelastic thin sheets

We show that a viscoelastic thin sheet driven out of equilibrium by active structural remodelling develops a rich variety of shapes as a result of a competition between viscous relaxation and activity. In the regime where active processes are faster than viscoelastic relaxation, wrinkles that are formed due to remodelling are unable to relax to a configuration that minimises the elastic energy and the sheet is inherently out of equilibrium. We argue that this non-equilibrium regime is of particular interest in biology as it allows the system to access morphologies that are unavailable if restricted to the adiabatic evolution between configurations that minimise the elastic energy alone. Here, we introduce activity using the formalism of evolving target metric and showcase the diversity of wrinkling morphologies arising from out of equilibrium dynamics.

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.

cond-mat.soft↗

arXiv2017

Stiffening Thermal Membranes by Cutting

Two-dimensional crystalline membranes have recently been realized experimentally in such systems as graphene and molybdenum disulfide, sparking a resurgence in interest in their statistical properties. Thermal fluctuations can significantly affect the effective mechanical properties of properly thermalized membranes, renormalizing both bending rigidity and elastic moduli so that in particular they become stiffer to bending than their bare bending rigidity would suggest. We use molecular dynamics simulations to examine how the mechanical behavior of thermalized two-dimensional clamped ribbons (cantilevers) depends on their precise topology and geometry. We find that a simple slit smooths roughness as measured by the variance of height fluctuations. This counterintuitive effect may be due to the counter-posed coupling of the lips of the slit to twist in the intact regions of the ribbon.

cond-mat.soft↗

arXiv2017

Dynamical patterns in active nematics on a sphere

Using agent-based simulations of self-propelled particles subject to short-range repulsion and nematic alignment we explore the dynamical phases of a dense active material confined to the surface of a sphere. We map the dynamical phase diagram as a function of curvature, alignment strength and activity and reproduce phases seen in recent experiments on active microtubules moving on the surfaces of vesicles. At low driving, we recover the equilibrium nematic ground state with four +1/2 defects. As the driving is increased, geodesic forces drive the transition to a band of polar matter wrapping around an equator, with large bald spots corresponding to two +1 defects at the poles. Finally, bands fold onto themselves, followed by the system moving into a turbulent state marked by active proliferation of pairs of topological defects. We highlight the role of nematic persistence length and time for pattern formation in these confined systems with finite curvature.

cond-mat.soft↗