arXiv subjects

Andrej Košmrlj

Publications and source records attributed to Andrej Košmrlj.

12 recordsLinked to original sources

arXiv2026

Dynamic Instabilities and Pattern Formation in Chemotactic Active Matter

Collectives of actively-moving particles can spontaneously segregate into dilute and dense phases through a process known as motility-induced phase separation (MIPS). This captivating phenomenon is well-studied for randomly-moving particles with no directional bias. However, many active systems perform collective chemotaxis -- directed motion along a chemical gradient collectively generated by the particles themselves through consumption or production. Here, we use linear stability analysis, amplitude equations, and numerical simulations to study how MIPS is influenced by collective chemotaxis. We find that chemotaxis can either arrest or entirely suppress MIPS, or give rise to novel dynamic instabilities such as traveling waves and spirals. We predict the stability region of the stationary and oscillatory patterns and identify four types of bifurcation that can arise: pitchfork, saddle-node, infinite period, and supercritical Hopf. We also derive analytical expressions for the amplitude of the pattern and traveling wave velocity, yielding excellent quantitative agreement with simulations. Furthermore, we generalize our model to study particles that either consume or produce chemoattractant or chemorepellent, as well as mixtures of particles with different chemotactic behaviors. By establishing quantitative principles describing the competition between MIPS and chemotaxis, our study helps deepen understanding of the rich physics underlying chemically-responsive active matter systems.

cond-mat.soft↗

arXiv2025

Predicting the Interfacial Energy and Morphology of DNA Condensates

The physics and morphology of biomolecular condensates formed through liquid-liquid phase separation underpin diverse biological processes, exemplified by the nested organization of nucleoli that facilitates ribosome biogenesis. Here, we develop a theoretical and computational framework to understand and predict multiphase morphologies in DNA-nanostar solutions. Because morphology is governed by interfacial energies between coexisting phases, we combine Flory-Huggins theory with coarse-grained molecular dynamics simulations to examine how these energies depend on key microscopic features of DNA nanostars, including size, valence, bending rigidity, Debye screening length, binding strength, and sticky-end distribution. The phase behavior of DNA nanostars is quantitatively captured by a generalized lattice model, in which the interplay between sticky-end binding energy and conformational entropy determines the effective interactions. Focusing on condensates comprising two dense phases, we find that Janus-like morphologies are ubiquitous because the interfacial energies between the dense and dilute phases, $γ_{i\in\{1,2\}}$, are typically comparable. In contrast, nested morphologies are rare as they require a large asymmetry in $γ_i$, which arises only for highly dissimilar nanostars such as those differing markedly in valence or size. Moreover, the interfacial energy between the two dense phases, $γ_{12}$, can be modulated either discretely, by varying sticky-end distribution, or continuously, by tuning the crosslinker ratio; the former may even eliminate nested configurations. These findings establish physical design principles for constructing complex condensate architectures directly from microscopic molecular parameters.

physics.bio-ph↗

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

Beaded metamaterials

From the pragmatic to the symbolic, textiles play a prominent role in some of the most demanding yet ubiquitous scenarios, such as covering the complex and dynamic geometries of the human body. Textiles are made by repeated manipulations of slender fibers into structures with emergent properties. Today, these ancient metamaterials are being examined in a new light, propelled by the idea that their geometric structures can be leveraged to engineer functional soft materials. However, per their inherent softness, textiles and other compliant materials cannot typically withstand compressive forces. This limitation hinders the transfer of soft matter's rich shape-morphing capabilities to broader research areas that require load-bearing capabilities. Here we introduce \textit{beading} as a versatile platform that links centuries of human ingenuity encoded in the world of textiles with the current demand for smart, programmable materials. By incorporating discrete rigid units, i.e. \textit{beads}, into various fiber-based assemblies, beadwork adds tunable stiffness to otherwise flaccid fabrics, creating new opportunities for textiles to become load-bearing. We select a shell-like bead design as a model experimental system and thoroughly describe how its mechanics are captured by friction, the material properties of the constituent elements, and geometry. The fundamental characterization in this study demonstrates the range of complex behaviors possible with this class of material, inspiring the application of soft matter principles to fields that ultimately demand rigidity, such as robotics and architecture.

cond-mat.soft↗

arXiv2024

Obstructed swelling and fracture of hydrogels

Obstructions influence the growth and expansion of bodies in a wide range of settings -- but isolating and understanding their impact can be difficult in complex environments. Here, we study obstructed growth/expansion in a model system accessible to experiments, simulations, and theory: hydrogels swelling around fixed cylindrical obstacles with varying geometries. When the obstacles are large and widely-spaced, hydrogels swell around them and remain intact. In contrast, our experiments reveal that when the obstacles are narrow and closely-spaced, hydrogels fracture as they swell. We use finite element simulations to map the magnitude and spatial distribution of stresses that build up during swelling at equilibrium in a 2D model, providing a route toward predicting when this phenomenon of self-fracturing is likely to arise. Applying lessons from indentation theory, poroelasticity, and nonlinear continuum mechanics, we also develop a theoretical framework for understanding how the maximum principal tensile and compressive stresses that develop during swelling are controlled by obstacle geometry and material parameters. These results thus help to shed light on the mechanical principles underlying growth/expansion in environments with obstructions.

cond-mat.soft↗

arXiv2023

Pattern formation of phase-separated lipid domains in bilayer membranes

Giant unilamellar vesicles (GUVs) composed of as few as three lipid species can phase separate into small-scale lipid domains with stripes and dots patterns. These patterns have been experimentally characterized in terms of how their size and morphology depend on temperature, membrane composition, and surface tension, which revealed inconsistencies with existing theoretical models. Here, we demonstrate that the experiments can be explained with a theory that considers both the elastic deformation of the membrane and the phase separation of lipids, which are coupled by a preferred bilayer curvature. We combine analytical and numerical approaches to elucidate how characteristic pattern size and morphology emerge from these interactions. The results agree with existing experiments and offer testable predictions such as non-monotonic dependence of the domain size on osmotic pressure and pattern hysteresis upon cycling external stimuli. These predictions motivate new directions for understanding the spatial patterning and organization mechanisms of biological membranes.

cond-mat.soft↗

arXiv2023

A New Perspective on Thermally Fluctuating 2D Elastic Membranes: Introducing Odd Elastic Moduli and Non-Equilibrium Effects

Non-equilibrium and active effects in mesoscopic scale systems have heralded a new era of scientific inquiries, whether concerning meta-materials or biological systems such as bacteria and cellular components. At mesoscopic scales, experimental and theoretical treatments of membranes, and other quasi-two-dimensional elastic surfaces cannot generically ignore Brownian motion and other thermal effects. In this paper we aim to study the behavior of thermally fluctuating 2-D elastic membranes possessing odd elastic moduli embedded in higher dimensions. We implement an isotropic generalization of the elastic tensor that includes odd elastic moduli, $K_{odd}$ and $A_{odd}$, that break conservation of energy and angular momentum respectively, due to cite{scheibner2020odd}. Naturally this introduces active and non-equilibrium effects. Passive equilibrium thermalized elastic membranes possess effective (renormalized) Lamé coefficients that reduce with increasing system size and a diverging effective bending rigidity. Introducing two odd elastic moduli means that deformations from a reference state can induce chiral forces that cannot be derived from a Hamiltonian. Thus, the behavior of odd elastic membranes must instead be investigated with Langevin equations. If fluctuation-dissipation relations hold, we calculate via the renormalization group that at long length scales, active effects due to $K_{odd}$ can be effectively ignored whereas $A_{odd}$ cannot. To validate these findings, we developed an advanced force implementation methodology, inspired by the $(T)$-scheme prevalent in vertex models. This contributed to a new method for the simulation of elastic membranes in higher dimensions, as detailed recently in \cite{matoz2020wrinkle}. The novelty of the method is that microscopic/discrete and continuum in-plane elastic moduli are one-to-one and thus no coarse-graining is needed.

cond-mat.soft↗

arXiv2023

Statistical mechanics of nanotubes

We investigate the effect of thermal fluctuations on the mechanical properties of nanotubes by employing tools from statistical physics. For 2D sheets it was previously shown that thermal fluctuations effectively renormalize elastic moduli beyond a characteristic temperature-dependent thermal length scale (a few nanometers for graphene at room temperature), where the bending rigidity increases, while the in-plane elastic moduli reduce in a scale-dependent fashion with universal power law exponents. However, the curvature of nanotubes produces new phenomena. In nanotubes, competition between stretching and bending costs associated with radial fluctuations introduces a characteristic elastic length scale, which is proportional to the geometric mean of the radius and effective thickness. Beyond elastic length scale, we find that the in-plane elastic moduli stop renormalizing in the axial direction, while they continue to renormalize in the circumferential direction beyond the elastic length scale albeit with different universal exponents. The bending rigidity, however, stops renormalizing in the circumferential direction at the elastic length scale. These results were verified using molecular dynamics simulations.

cond-mat.stat-mech↗

arXiv2023

Chemotactic motility-induced phase separation

Collectives of actively-moving particles can spontaneously separate into dilute and dense phases -- a fascinating phenomenon known as motility-induced phase separation (MIPS). MIPS is well-studied for randomly-moving particles with no directional bias. However, many forms of active matter exhibit collective chemotaxis, directed motion along a chemical gradient that the constituent particles can generate themselves. Here, using theory and simulations, we demonstrate that collective chemotaxis strongly competes with MIPS -- in some cases, arresting or completely suppressing phase separation, or in other cases, generating fundamentally new dynamic instabilities. We establish quantitative principles describing this competition, thereby helping to reveal and clarify the rich physics underlying active matter systems that perform chemotaxis, ranging from cells to robots.

physics.bio-ph↗

arXiv2022

Mechanical Properties Of Fluctuating Elastic Membranes Under Uni-Axial Tension

Atomically thin sheets, such as graphene, are widely used in nanotechnology. Recently they have also been used in applications including kirigami and self-folding origami, where it becomes important to understand how they respond to external loads. Motivated by this, we investigate how isotropic sheets respond to uniaxial tension by employing the self-consistent screening analysis method and molecular dynamics simulations. Previously, it was shown that for freely suspended sheets thermal fluctuations effectively renormalize elastic constants, which become scale-dependent beyond a characteristic thermal length scale (a few nanometers for graphene at room temperature), beyond which the bending rigidity increases, while the in-plane elastic constants reduce with universal power law exponents. For sheets under uniaxial tension, $σ_{11}$, we find that beyond a stress-dependent length scale, the effective in-plane elastic constants become strongly anisotropic and scale differently along the axis of uni-axial stress and orthogonal to it. The bending rigidities on the other hand will not exhibit any anomalous behavior beyond this stress-dependent length scale. In addition, for moderate tensions we find a universal non-linear stress-strain relation. For large uni-axial tensions, the Young's modulus of the bare elastic material is recovered.

cond-mat.stat-mech↗

arXiv2021

Liquid demixing in elastic networks: cavitation, permeation, or size selection?

Demixing of multicomponent biomolecular systems via liquid-liquid phase separation (LLPS) has emerged as a potentially unifying mechanism governing the formation of several membrane-less intracellular organelles ("condensates"), both in the cytoplasm (e.g., stress granules) and in the nucleoplasm (e.g., nucleoli). While both in vivo experiments and studies of synthetic systems demonstrate that LLPS is strongly affected by the presence of a macromolecular elastic network, a fundamental understanding of the role of such networks on LLPS is still lacking. Here we show that, upon accounting for capillary forces responsible for network expulsion, small-scale heterogeneity of the network, and its nonlinear mechanical properties, an intriguing picture of LLPS emerges. Specifically, we predict that, in addition to the experimentally observed cavitated droplets which fully exclude the network, two other phases are thermodynamically possible: elastically arrested, size-limited droplets at the network pore scale, and network-including macroscopic droplets. In particular, pore size-limited droplets may emerge in chromatin networks, with implications for structure and function of nucleoplasmic condensates.

cond-mat.soft↗

arXiv2020

Finite Temperature Phase Behavior of Viral Capsids as Oriented Particle Shells

A general phase-plot is proposed for discrete particle shells that allows for thermal fluctuations of the shell geometry and of the inter-particle connectivities. The phase plot contains a first-order melting transition, a buckling transition and a collapse transition and is used to interpret the thermodynamics of microbiological shells.

physics.comp-ph↗