arXiv subjects

Luca Giomi

Publications and source records attributed to Luca Giomi.

At least 19 recordsLinked to original sources

arXiv2026

Multiscale order, flocking and phenotypic hysteresis in the cellular Potts model of epithelia

In epithelia, how do collective cell migration and tissue spatial organization feedback on each other? We address this question through large-scale numerical simulations of the cellular Potts model. By accounting for both cell morphology and cytoskeletal activity, we uncover a remarkably rich phase diagram featuring multiple types of orientational order, either as distinct phases or coexisting across length scales. We identify a specific pathway in parameter space along which a gradual increase in the actin polymerization rate drives a phase transition into a long-range flocking state. Simultaneously, quasi-long-range nematic order emerges at length scales much larger than the cell size due to the combined effects of directed motion and lateral cell-cell interactions. At length scales comparible to cell size, however, cells adopt an approximatively hexagonal morphology, resulting in hexanematic order, similar to that observed in reconstituted Madin-Darby Canine Kidney (MDCK) cell monolayers. With further increases in actin polymerization, nematic order becomes fully long-range, while hexatic order remains quasi-long-range and confined to short length scales, but independent of cytoskeletal activity. When noise is sufficiently low to allow crystallization at finite actin polymerization rate, cycling the cell-monolayer across the melting transition yields an example of phenotypical hysteresis, reminiscent of that observed across the epithelial-mesenchymal transition.

cond-mat.soft↗

arXiv2026

Shaping nematic order in bacterial films with single-cell resolution patterning

Bacterial colonies composed of elongated cells form active nematic fluids that spontaneously self-organise into ordered domains of aligned cells and exhibit self-generated chaotic flows powered by cell growth. While their dynamics have attracted significant attention, the role of initial conditions remains largely unexplored due to a lack of precise patterning methods. Here, we harness the precision of capillary assembly to pattern Bacillus subtilis endospores into arrays with controlled positions and orientations at single-cell resolution. Upon germination and growth of cell chains, we quantify the dynamics and morphologies of the resulting bacterial films. While orthogonally seeded spores lead to chaotic dynamics, seeding them with parallel orientations yields films with high nematic order across millimetres, which subsequently synchronously buckle upon further growth. Our observations are captured by numerical simulations and a model that describes the buckling dynamics starting from the mechanical properties of individual filaments. By programming local cell orientation with single-cell precision, we finally harness nematic alignment to create macroscopic bacterial films with local optical anisotropy, via structural colouration and light polarisation. Our findings demonstrate that initial conditions play a key role and offer exciting opportunities to control the spatio-temporal organization of bacterial assemblies towards addressing open biological questions and realizing living materials with tailored properties.

physics.bio-ph↗

arXiv2026

Mechanics of axis formation in $\textit{Hydra}$

The emergence of a body axis is a fundamental step in the development of multicellular organisms. In simple systems such as $\textit{Hydra}$, growing evidence suggests that mechanical forces generated by collective cellular activity play a central role in this process. Here, we explore a physical mechanism for axis formation based on the coupling between active stresses and tissue elasticity. We analyse the elastic deformation induced by activity-generated stresses and show that, owing to the spherical topology of the tissue, forces globally condense toward configurations in which both elastic strain and nematic defect localise at opposite poles. These mechanically selected states define either a polar or apolar head-food axis. To characterize the condensed regime, we introduce a compact parametrization of of the active force and flux distributions, enabling analytical predictions and direct comparison with experiments. Using this framework, we calculate experimentally relevant observables, including areal strain, lateral pressure, and normal displacements during muscular contraction, as well as the detailed structure of topological defect complexes in head and foot regions. Together, our results identify a mechanical route by which active tissues can spontaneously break symmetry at the organismal scale, suggesting a general physical principle underlying body-axis specification during morphogenesis.

cond-mat.soft↗

arXiv2025

Hydrodynamic stability and pattern formation in hexatic epithelial layers

We investigate the hydrodynamic stability and the formation of patterns in a continuum model of epithelial layers, able to account for the interplay between mechanical activity, lateral adhesion and the $6-$fold orientational order originating from the hexagonal morphology of the cells. Unlike in other models of active liquid crystals, the balance between energy injection and dissipation can here involve multiple length scales, resulting in a large spectrum of dynamical behaviors. When kinetic energy is dissipated by the cells' adhesive interactions at a rate higher that at which is injected by active stresses, the quiescent state of the cellular layer is generically stable: i.e. hydrodynamically stable regardless of its size. On the other hand, as the cellular layer becomes progressively more active, this homeostatic condition is altered by a hierarchy of pattern-forming instabilities, where the system organizes in an increasingly large number of counter-flowing lanes of fixed width. In two-dimensional periodic domains, the latter organization is itself unstable to the proliferation of vortices and the dynamics of the cellular layer becomes eventually chaotic and yet different from the more common active turbulence.

cond-mat.soft↗

arXiv2025

Stretching theory of Hookean metashells

Despite being governed by the familiar laws of Hookean mechanics, elastic shells patterned with an internal structure (i.e. metashells) exhibit a wealth of unusual mechanical properties with no counterparts in unstructured materials. Here I show that much of this behavior can be captured by a real-valued analog of the inhomogeneous Schr\"odinger equation, with the lateral pressure experienced by the internal structure in the role of the wave function. In the fine structure limit $-$ i.e. when the length scale associated with the internal structure is much smaller than the local radius of curvature $-$ this approach reveals the existence of localized states, in which elastic deformations are prevented to diffuse away from their origin, thereby allowing the internal structure to smoothly adapt to the intrinsic geometry of the metashell. Leveraging on an analogy with scattering states in nearly free electrons, I further show that periodic metashells, obtained from the repetition of the same structural unit periodically in space, support elastic Bloch waves, corresponding to stationary periodic configurations of the internal structure and characterized by a geometry-dependent band structure. When applied to crystalline monolayers, this approach provides a generalization of the elastic theory of interacting topological defect to compressible systems.

cond-mat.soft↗

arXiv2025

Collective migration and topological phase transitions in confluent epithelia

Collective epithelial migration leverages on topological rearrangements of the intercellular junctions, which allow cells to intercalate without loosing confluency. In silico studies have provided a clear indication that this process could occur via a two-step phase transition, where a hierarchy of topological excitations progressively transforms an epithelial layer from a crystalline solid to an isotropic liquid, via an intermediate hexatic liquid crystal phase. Yet, the fundamental mechanism behind this process and its implications for collective cell behavior are presently unknown. In this article, we show that the onset of collective cell migration in cell-resolved models of epithelial layers takes place via an activity-driven melting transition, characterized by an exponentially-divergent correlation length across the solid/hexatic phase boundary. Using a combination of numerical simulations and Renormalization Group analysis, we show that the availability of topologically distinct rearrangements - known as T1 and T2 processes - and of a non-thermal route to melting, renders the transition significantly more versatile and tunable than in two-dimensional passive matter. Specifically, the relative frequency of T1 and T2 processes and of the "bare" stiffness of the cell layer affect the divergence of positional correlations within a well-defined spectrum of critical behaviors. Suppressing T1 processes, changes the nature of the transition by preventing collective migration in favor of a cellular analog of surface sublimation.

cond-mat.soft↗

arXiv2023

Quasi long-ranged order in two-dimensional active liquid crystals

Quasi-long ranged order is the hallmark of two-dimensional liquid crystals. At equilibrium, this property implies that the correlation function of the local orientational order parameter decays with distance as a power law: i.e. $\sim|\boldsymbol{r}|^{-\eta_{p}}$, with $\eta_{p}$ a temperature-dependent exponent. While in general non-universal, $\eta_{p}=1/4$ universally at the Berezinskii-Kosterlitz-Thouless transition, where orientational order is lost because of the unbinding of disclinations. Motivated by recent experimental findings of liquid crystal order in confluent cell monolayers, here we demonstrate that, in {\em active} liquid crystals, the notion of quasi-long ranged order fundamentally differs from its equilibrium counterpart and is ultimately dictated by the interplay between translational and orientational dynamics. As a consequence, the exponent $\eta_{p}$ is allowed to vary in the range $0<\eta_{p}\le 2$, with the upper bound corresponding to the isotropic phase. Our theoretical predictions are supported by a survey of recent experimental data, reflecting a wide variety of different realization of orientational order in two dimensions.

cond-mat.soft↗

arXiv2023

Designing highly efficient lock-and-key interactions in anisotropic active particles

Cluster formation of microscopic swimmers is key to the formation of biofilms and colonies, efficient motion and nutrient uptake, but, in the absence of other interactions, requires high swimmer concentrations to occur. Here we experimentally and numerically show that cluster formation can be dramatically enhanced by an anisotropic swimmer shape. We analyze a class of model microswimmers with a shape that can be continuously tuned from spherical to bent and straight rods. In all cases, clustering can be described by Michaelis-Menten kinetics governed by a single scaling parameter that depends on particle density and shape only. We rationalize these shape-dependent dynamics from the interplay between interlocking probability and cluster stability. The bent rod shape promotes assembly even at vanishingly low particle densities and we identify the most efficient shape to be a semicircle. Our work provides key insights into how shape can be used to rationally design out-of-equilibrium self-organization, key to creating active functional materials and designing targeted two-component drug delivery.

cond-mat.soft↗

arXiv2023

Theory of cellular homochirality and trait evolution in flocking systems

Chirality is a feature of many biological systems and much research has been focused on understanding the origin and implications of this property. Famously, sugars and amino acids found in nature are homochiral, i.e., chiral symmetry is broken and only one of the two possible chiral states is ever observed. Certain types of cells show chiral behavior, too. Understanding the origin of cellular chirality and its effect on tissues and cellular dynamics is still an open problem and subject to much (recent) research, e.g., in the context of drosophila morphogenesis. Here, we develop a simple model to describe the possible origin of homochirality in cells. Combining the Vicsek model for collective behavior with the model of Jafarpour et al., developed to describe the emergence of molecular homochirality, we investigate how a homochiral state might have evolved in cells from an initially symmetric state without any mechanisms that explicitly break chiral symmetry. We investigate the transition to homochirality and show how the "openness" of the system as well as noise determine if and when a globally homochiral state is reached. We discuss how our model can be applied to the evolution of traits in flocking systems in general, or to study systems consisting of multiple interacting species.

q-bio.CB↗

arXiv2023

Collective epithelial migration mediated by the unbinding of hexatic defects

Collective cell migration in epithelia relies on cell intercalation: a local remodelling of the cellular network that allows neighbouring cells to swap their positions. Unlike foams and passive cellular fluid, in epithelial intercalation these rearrangements crucially depend on activity. During these processes, the local geometry of the network and the contractile forces generated therein conspire to produce a burst of remodelling events, which collectively give rise to a vortical flow at the mesoscopic length scale. In this article we formulate a continuum theory of the mechanism driving this process, built upon recent advances towards understanding the hexatic (i.e. $6-$fold ordered) structure of epithelial layers. Using a combination of active hydrodynamics and cell-resolved numerical simulations, we demonstrate that cell intercalation takes place via the unbinding of topological defects, naturally initiated by fluctuations and whose late-times dynamics is governed by the interplay between passive attractive forces and active self-propulsion. Our approach sheds light on the structure of the cellular forces driving collective migration in epithelia and provides an explanation of the observed extensile activity of in vitro epithelial layers.

cond-mat.soft↗

arXiv2022

Polymorphism in tubulin assemblies: a mechanical model

We investigate the mechanical origin of polymorphic structures in two-dimensional tubulin assemblies, of which microtubules are the best known example. These structures feature twisted ribbons, flat tubulin sheets, macrotubules, and hoops, and they spontaneously assemble depending on the chemical environment. Upon modelling tubulin aggregates as minimally anisotropic elastic shells and using a combination of numerical simulations and analytical work, we show that the mechanical strain in tubulin lattices, originating from asymmetries at the single dimer level, naturally gives rise to polymorphic assemblies, among which cylinders and other tubular structures are predominant for a wide range of values of spontaneous curvature. Furthermore, our model suggests that switching the sign of the sheets' spontaneous Gaussian curvature from positive (i.e. sphere-like) to negative (i.e. saddle-like), could provide a possible route to microtubules disassembly.

cond-mat.soft↗

arXiv2022

Tuneable defect-curvature coupling and topological transitions in active shells

Recent experimental observations have suggested that topological defects can facilitate the creation of sharp features in developing embryos. Whereas these observations echo established knowledge about the interplay between geometry and topology in two-dimensional passive liquid crystals, the role of activity has mostly remained unexplored. In this article we focus on deformable shells consisting of either polar or nematic active liquid crystals and demonstrate that activity renders the mechanical coupling between defects and curvature much more involved and versatile than previously thought. Using a combination of linear stability analysis and three-dimensional computational fluid dynamics, we demonstrate that such a coupling can in fact be tuned, depending on the type of liquid crystal order, the specific structure of the defect (i.e. asters or vortices) and the nature of the active forces. In polar systems, this can drive a spectacular transition from spherical to toroidal topology, in the presence of large extensile activity. Our analysis strengthens the idea that defects could serve as topological morphogens and provides a number of predictions that could be tested in in vitro studies, for instance in the context of organoids.

cond-mat.soft↗

arXiv2022

Hydrodynamic Enhancement of $p$-atic Defect Dynamics

We investigate numerically and analytically the effects of hydrodynamics on the dynamics of topological defects in $p-$atic liquid crystals, i.e. two-dimensional liquid crystals with $p-$fold rotational symmetry. Importantly, we find that hydrodynamics fuels a generic passive self-propulsion mechanism for defects of winding number $s=(p-1)/p$ and arbitrary $p$. Strikingly, we discover that hydrodynamics always accelerates the annihilation dynamics of pairs of $\pm 1/p$ defects, and that, contrary to expectations, this effect increases with $p$. Our Letter paves the way towards understanding cell intercalation and other remodelling events in epithelial layers.

cond-mat.soft↗

arXiv2022

Hydrodynamics and multiscale order in confluent epithelia

We formulate a hydrodynamic theory of confluent epithelia: i.e. monolayers of epithelial cells adhering to each other without gaps. Taking advantage of recent progresses toward establishing a general hydrodynamic theory of p-atic liquid crystals, we demonstrate that collectively migrating epithelia feature both nematic (i.e. p=2) and hexatic (i.e. p=6) order, with the former being dominant at large and the latter at small length scales. Such a remarkable multiscale liquid crystal order leaves a distinct signature in the system's structure factor, which exhibits two different power law scaling regimes, reflecting both the hexagonal geometry of small cells clusters, as well as the uniaxial structure of the global cellular flow. We support these analytical predictions with two different cell-resolved models of epithelia -- i.e. the self-propelled Voronoi model and the multiphase field model -- and highlight how momentum dissipation and noise influence the range of fluctuations at small length scales, thereby affecting the degree of cooperativity between cells. Our construction provides a theoretical framework to conceptualize the recent observation of multiscale order in layers of Madin-Darby canine kidney cells and pave the way for further theoretical developments.

cond-mat.soft↗

arXiv2022

Epithelia are multiscale active liquid crystals

Biological processes such as embryogenesis, wound healing and cancer progression, crucially rely on the ability of epithelial cells to coordinate their mechanical activity over length scales order of magnitudes larger than the typical cellular size. While regulated by various signalling pathways, it has recently become evident that this behavior can additionally hinge on a minimal toolkit of physical mechanisms, of which liquid crystal order is the most prominent example. Yet, experimental and theoretical studies have given so far inconsistent results in this respect: whereas nematic order is often invoked in the interpretation of experimental data, computational models have instead suggested that hexatic order could serve as a linchpin for collective migration in confluent cell layers. In this article we resolve this dilemma. Using a combination of in vitro experiments on Madin-Darby canine kidney cells (MDCK), numerical simulations and analytical work, we demonstrate that both nematic and hexatic order are, in fact, present in epithelial layers, with the former being dominant at large length scales and the latter at small length scales. In MDCK GII cells on uncoated glass, these different types of liquid crystal order crossover at a length scale of the order of ten cell sizes. Our work sheds light on the emergent organization of living matter, provides a new framework for deciphering the structure of epithelia, and paves the way toward a comprehensive and predictive mesoscopic theory of tissues.

cond-mat.soft↗

arXiv2021

Statistics and Topology of Fluctuating Ribbons

Ribbons are a class of slender structures whose length, width, and thickness are widely separated from each other. This scale separation gives a ribbon unusual mechanical properties in athermal macroscopic settings, e.g. it can bend without twisting, but cannot twist without bending. Given the ubiquity of ribbon-like biopolymers in biology and chemistry, here we study the statistical mechanics of microscopic inextensible, fluctuating ribbons loaded by forces and torques. We show that these ribbons exhibit a range of topologically and geometrically complex morphologies exemplified by three phases - a twist-dominated helical phase (HT), a writhe-dominated helical phase (HW), and an entangled phase - that arise as the applied torque and force is varied. Furthermore, the transition from HW to HT phases is characterized by the spontaneous breaking of parity symmetry and the disappearance of perversions that characterize chirality reversals. This leads to a universal response curve of a topological quantity, the link, as a function of the applied torque that is similar to magnetization curves in second-order phase transitions.

cond-mat.stat-mech↗

arXiv2021

Long-ranged order and flow alignment in sheared $p-$atic liquid crystals

We formulate a hydrodynamic theory of $p-$atic liquid crystals, namely two-dimensional anisotropic fluids endowed with generic $p-$fold rotational symmetry. Our approach, based on an order parameter tensor that directly embodies the discrete rotational symmetry of $p-$atic phases, allows us to unveil several unknown aspects of flowing $p-$atics, that previous theories, characterized by ${\rm O(2)}$ rotational symmetry, could not account for. This includes the onset of long-ranged orientational order in the presence of a simple shear flow of arbitrary shear rate, as opposed to the standard quasi-long-ranged order of two-dimensional liquid crystals, and the possibility of flow alignment at large shear rates.

cond-mat.soft↗

arXiv2021

Self-assembly dynamics of reconfigurable colloidal molecules

Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby restricting their use as model systems. We overcome this limitation by assembling reconfigurable colloidal molecules from silica particles functionalized with mobile DNA linkers in high yields. We achieve this by steering the self-assembly pathway towards the formation of finite-sized clusters by employing high number ratios of particles functionalized with complementary DNA strands. The size ratio of the two species of particles provides control over the overall cluster size, or, "valence", as well as the degree of reconfigurability. The bond flexibility provided by the mobile linkers allows the successful assembly of colloidal clusters with the geometrically expected maximum valence. We quantitatively examine the self-assembly dynamics of these flexible colloidal molecules by a combination of experiments, molecular dynamics simulations, and an analytical model. Our "flexible colloidal molecules" are exciting building blocks for investigating and exploiting the self-assembly of complex hierarchical structures, photonic crystals and colloidal meta-materials.

cond-mat.soft↗