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Luca Giomi

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Published work

25 published item(s)

preprint2026arXiv

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.

preprint2026arXiv

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.

preprint2022arXiv

Theory of defect-mediated morphogenesis

Growing experimental evidence indicates that topological defects could serve as organizing centers in the morphogenesis of tissues. Here, we provide a quantitative explanation for this phenomenon, rooted in the buckling theory of deformable active polar liquid crystals. Using a combination of linear stability analysis and computational fluid dynamics, we demonstrate that active layers, such as confined cell monolayers, are unstable to the formation of protrusions in the presence of disclinations. The instability originates from an interplay between the focusing of the elastic forces, mediated by defects, and the renormalization of the system's surface tension by the active flow. The posttransitional regime is also characterized by several complex morphodynamical processes, such as oscillatory deformations, droplet nucleation, and active turbulence. Our findings offer an explanation of recent observations on tissue morphogenesis and shed light on the dynamics of active surfaces in general.

preprint2021arXiv

Confinement-induced self-organization in growing bacterial colonies

We investigate the emergence of global alignment in colonies of dividing rod-shaped cells under confinement. Using molecular dynamics simulations and continuous modeling, we demonstrate that geometrical anisotropies in the confining environment give rise to imbalance in the normal stresses, which, in turn, drives a collective rearrangement of the cells. This behavior crucially relies on the colony's solid-like mechanical response at short time scales and can be recovered within the framework of active hydrodynamics upon modeling bacterial colonies as growing viscoelastic gels characterized by Maxwell-like stress relaxation.

preprint2021arXiv

Hydrodynamic theory of $p-$atic liquid crystals

We formulate a comprehensive hydrodynamic theory of two-dimensional liquid crystals with generic $p-$fold rotational symmetry, also known as $p-$atics, of which mematics $(p=2)$ and hexatics $(p=6)$ are the two best known examples. Previous hydrodynamic theories of $p-$atics are characrerized by continuous ${\rm O}(2)$ rotational symmetry, which is higher than the discrete rotational symmetry of $p-$atic phases. By contrast, here we demonstrate that the discrete rotational symmetry allows the inclusion of additional terms in the hydrodynamic equations, which, in turn, lead to novel phenomena, such as the possibility of flow alignment at high shear rates, even for $p>2$. Furthermore, we show that any finite imposed shear will induce long-ranged orientational order in any $p-$atic liquid crystal, in contrast to the quasi-long-ranged order that occurs in the absence of shear. The induced order parameter scales like a non-universal power of the applied shear rate at small shear rates.

preprint2021arXiv

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.

preprint2021arXiv

Metastability of lipid necks via geometric triality

"Necks" are features of lipid membranes characterized by an uniquley large curvature, functioning as bridges between different compartments. These features are ubiquitous in the life-cycle of the cell and instrumental in processes such as division, extracellular vesicles uptake and cargo transport between organelles, but also in life-threatening conditions, as in the endocytosis of viruses and phages. Yet, the very existence of lipid necks challenges our understanding of membranes biophysics: their curvature, often orders of magnitude larger than elsewhere, is energetically prohibitive, even with the arsenal of molecular machineries and signalling pathways that cells have at their disposal. Using a geometric triality, namely a correspondence between three different classes of geometric objects, here we demonstrate that lipid necks are in fact metastable, thus can exist for finite, but potentially long times even in the absence of stabilizing mechanisms. This framework allows us to explicitly calculate the forces a corpuscle must overcome in order to penetrate cellular membranes, thus paving the way for a predictive theory of endo/exo-cytic processes.

preprint2021arXiv

Supported lipid membranes with designed geometry

The membrane curvature of cells and intracellular compartments continuously adapts to enable cells to perform vital functions, from cell division to signal trafficking. Understanding how membrane geometry affects these processes in vivo is challenging because of the membrane complexity as well as the short time and small length scales involved. By contrast, in vitro model membranes with engineered curvature provide a versatile platform for this investigation and applications to biosensing and biocomputing. However, a general route to the fabrication of lipid membranes with prescribed curvature and high spatial resolution is still missing. Here, we present a strategy that overcomes these challenges and achieve lipid membranes with designed shape by combining 3D micro-printing and replica-molding lithography to create scaffolds with virtually any geometry and high spatial resolution. The resulting supported lipid membranes are homogeneous, fluid, and can form chemically distinct lipid domains. These features are essential for understanding curvature-dependent cellular processes and developing programmable bio-interfaces for living cells and nanostructures.

preprint2020arXiv

Chiral stresses in nematic cell monolayers

Recent experiments on monolayers of spindle-like cells plated on adhesive stripe-shaped domains have provided a convincing demonstration that certain types of collective phenomena in epithelia are well described by active nematic hydrodynamics. While recovering some of the hallmark predictions of this framework, however, these experiments have also revealed a number of unexpected features that could be ascribed to the existence of chirality over length scales larger than the typical size of a cell. In this article we elaborate on the microscopic origin of chiral stresses in nematic cell monolayers and investigate how chirality affects the motion of topological defects, as well as the collective motion in stripe-shaped domains. We find that chirality introduces a characteristic asymmetry in the collective cellular flow, from which the ratio between chiral and non-chiral active stresses can be inferred by particle-image-velocimetry measurements. Furthermore, we find that chirality changes the nature of the spontaneous flow transition under confinement and that, for specific anchoring conditions, the latter has the structure of an imperfect pitchfork bifurcation.

preprint2020arXiv

Dislocation screening in crystals with spherical topology

Whereas disclination defects are energetically prohibitive in two-dimensional flat crystals, their existence is necessary in crystals with spherical topology, such as viral capsids, colloidosomes or fullerenes. Such a geometrical frustration gives rise to large elastic stresses, which render the crystal unstable when its size is significantly larger than the typical lattice spacing. Depending on the compliance of the crystal with respect to stretching and bending deformations, these stresses are alleviated by either a local increase of the intrinsic curvature in proximity of the disclinations or by the proliferation of excess dislocations, often organized in the form of one-dimensional chains known as "scars". The associated strain field of the scars is such to counterbalance the one resulting from the isolated disclinations. Here, we develop a continuum theory of dislocation screening in two-dimensional closed crystals with genus one. Upon modeling the flux of scars emanating from a given disclination as an independent scalar field, we demonstrate that the elastic energy of closed two-dimensional crystals with various degrees of asphericity can be expressed as a simple quadratic function of the screened topological charge of the disclinations, both at zero and finite temperature. This allows us to predict the optimal density of the excess dislocations as well as the minimal stretching energy attained by the crystal.

preprint2019arXiv

Lipid exchange enhances geometric pinning in multicomponent membranes on patterned substrates

Experiments on supported lipid bilayers featuring liquid ordered/disordered domains have shown that the spatial arrangement of the lipid domains and their chemical composition are strongly affected by the curvature of the substrate. Furthermore, theoretical predictions suggest that both these effects are intimately related with the closed topology of the bilayer. In this work, we test this hypothesis by fabricating supported membranes consisting of colloidal particles of various shapes lying on a flat substrate. A single lipid bilayer coats both colloids and substrate, allowing local lipid exchange between them, thus rendering the system thermodynamically open, i.e. able to exchange heat and molecules with an external reservoir in the neighborhood of the colloid. By reconstructing the Gibbs phase diagram for this system, we demonstrate that the free-energy landscape is directly influenced by the geometry of the colloid. In addition, we find that local lipid exchange enhances the pinning of the liquid disordered phase in highly curved regions. This allows us to provide estimates of the bending moduli difference of the domains. Finally, by combining experimental and numerical data, we forecast the outcome of possible experiments on catenoidal and conical necks and show that these geometries could greatly improve the precision of the current estimates of the bending moduli.

preprint2019arXiv

Topotaxis of active Brownian particles

Recent experimental studies have demonstrated that cellular motion can be directed by topographical gradients, such as those resulting from spatial variations in the features of a micropatterned substrate. This phenomenon, known as topotaxis, is especially prominent among cells persistently crawling within a spatially varying distribution of cell-sized obstacles. In this article we introduce a toy model of topotaxis based on active Brownian particles constrained to move in a lattice of obstacles, with space-dependent lattice spacing. Using numerical simulations and analytical arguments, we demonstrate that topographical gradients introduce a spatial modulation of the particles' persistence, leading to directed motion toward regions of higher persistence. Our results demonstrate that persistent motion alone is sufficient to drive topotaxis and could serve as a starting point for more detailed studies on self-propelled particles and cells.

preprint2016arXiv

Orientational properties of nematic disclinations

Topological defects play a pivotal role in the physics of liquid crystals and represent one of the most prominent and well studied aspects of mesophases. While in two-dimensional nematics, disclinations are traditionally treated as point-like objects, recent experimental studies on active nematics have suggested that half-strength disclinations might in fact possess a polar structure. In this article, we provide a precise definition of polarity for half-strength nematic disclinations, we introduce a simple and robust method to calculate this quantity from experimental and numerical data and we investigate how the orientational properties of half-strength disclinations affect their relaxational dynamics.

preprint2015arXiv

Geometry and topology of turbulence in active nematics

The problem of low Reynolds number turbulence in active nematic fluids is theoretically addressed. Using numerical simulations I demonstrate that an incompressible turbulent flow, in two-dimensional active nematics, consists of an ensemble of vortices whose areas are exponentially distributed within a range of scales. Building on this evidence, I construct a mean-field theory of active turbulence by which several measurable quantities, including the spectral densities and the correlation functions, can be analytically calculated. Because of the profound connection between the flow geometry and the topological properties of the nematic director, the theory sheds light on the mechanisms leading to the proliferation of topological defects in active nematics and provides a number of testable predictions. A hypothesis, inspired by Onsager's statistical hydrodynamics, is finally introduced to account for the equilibrium probability distribution of the vortex sizes.

preprint2014arXiv

Defect dynamics in active nematics

Topological defects are distinctive signatures of liquid crystals. They profoundly affect the viscoelastic behavior of the fluid by constraining the orientational structure in a way that inevitably requires global changes not achievable with any set of local deformations. In active nematic liquid crystals topological defects not only dictate the global structure of the director, but also act as local sources of motion, behaving as self-propelled particles. In this article we present a detailed analytical and numerical study of the mechanics of topological defects in active nematic liquid crystals.

preprint2014arXiv

On shape dependence of holographic mutual information in AdS4

We study the holographic mutual information in AdS4 of disjoint spatial domains in the boundary which are delimited by smooth closed curves. A numerical method which approximates a local minimum of the area functional through triangulated surfaces is employed. After some checks of the method against existing analytic results for the holographic entanglement entropy, we compute the holographic mutual information of equal domains delimited by ellipses, superellipses or the boundaries of two dimensional spherocylinders, finding also the corresponding transition curves along which the holographic mutual information vanishes.

preprint2014arXiv

Topology and Dynamics of Active Nematic Vesicles

Engineering synthetic materials that mimic the remarkable complexity of living organisms is a fundamental challenge in science and technology. We study the spatiotemporal patterns that emerge when an active nematicfilm of microtubules and molecular motors is encapsulated within a shape-changing lipid vesicle. Unlike in equilibrium systems, where defects are largely static structures, in active nematics defects move spontaneously and can be described as self-propelled particles. The combination of activity, topological constraints and vesicle deformability produces a myriad of dynamical states. We highlight two dynamical modes: a tunable periodic state that oscillates between two defect configurations, and shape-changing vesicles with streaming filopodia-like protrusions. These results demonstrate how biomimetic materials can be obtained when topological constraints are used to control the non-equilibrium dynamics of active matter.

preprint2013arXiv

Defect annihilation and proliferation in active nematics

Liquid crystals inevitably possess topological defect excitations generated through boundary conditions, applied fields or in quenches to the ordered phase. In equilibrium pairs of defects coarsen and annihilate as the uniform ground state is approached. Here we show that defects in active liquid crystals exhibit profoundly different behavior, depending on the degree of activity and its contractile or extensile character. While contractile systems enhance the annihilation dynamics of passive systems, extensile systems act to drive defects apart so that they swarm around in the manner of topologically well-characterized self-propelled particles. We develop a simple analytical model for the defect dynamics which reproduces the key features of both the numerical solutions and recent experiments on microtuble-kinesin assemblies.

preprint2013arXiv

Polymorphism and bistability in adherent cells

The optimal shapes attained by contractile cells on adhesive substrates are determined by the interplay between intracellular forces and adhesion with the extracellular matrix. We model the cell as a contractile film bounded by an elastic cortex and connected to the substrate via elastic links. When the adhesion sites are continuously distributed, optimal cell shape is constrained by the adhesion geometry, with a spread area sensitively dependent on the substrate stiffness and contractile tension. For discrete adhesion sites, equilibrium cell shape is convex at weak contractility, while developing local concavities at intermediate values of contractility. Increasing contractility beyond a critical value, controlled by mechanical and geometrical properties of adhesion, cell boundary undergoes a discontinuous transition to a star-shaped configuration with cusps and protrusions, accompanied by a region of bistability and hysteresis.

preprint2013arXiv

Softly Constrained Films

The shape of materials is often subject to a number of geometric constraints that limit the size of the system or fix the structure of its boundary. In soft and biological materials, however, these constraints are not always hard, but are due to other physical mechanisms that affect the overall force balance. A capillary film spanning a flexible piece of wire or a cell anchored to a compliant substrate by mean of adhesive contacts are examples of these softly constrained systems in the macroscopic and microscopic world. In this article I review some of the important mathematical and physical developments that contributed to our understanding of shape formation in softly constrained films and their recent application to the mechanics of adherent cells.

preprint2012arXiv

Hyperbolic Interfaces

Fluid interfaces, such as soap films, liquid droplets or lipid membranes, are known to give rise to several special geometries, whose complexity and beauty continue to fascinate us, as observers of the natural world, and challenge us as scientists. Here I show that a special class of surfaces of constant negative Gaussian curvature can be obtained in fluid interfaces equipped with an orientational ordered phase. These arise in various soft and biological materials, such as nematic liquid crystals, cytoskeletal assemblies, or hexatic colloidal suspensions. The purely hyperbolic morphology originates from the competition between surface tension, that reduces the area of the interface at the expense of increasing its Gaussian curvature, and the orientational elasticity of the ordered phase, that in turn suffers for the distortion induced by the underlying curvature.

preprint2011arXiv

Molecular Tilt on Monolayer-Protected Nanoparticles

The structure of the tilted phase of monolayer-protected nanoparticles is investigated by means of a simple Ginzburg-Landau model. The theory contains two dimensionless parameters representing the preferential tilt angle and the ratio epsilon between the energy cost due to spatial variations in the tilt of the coating molecules and that of the van der Waals interactions which favors uniform tilt. We analyze the model for both spherical and octahedral particles. On spherical particles, we find a transition from a tilted phase, at small epsilon, to a phase where the molecules spontaneously align along the surface normal and tilt disappears. Octahedral particles have an additional phase at small epsilon characterized by the presence of six topological defects. These defective configurations provide preferred sites for the chemical functionalization of monolayer-protected nanoparticles via place-exchange reactions and their consequent linking to form molecules and bulk materials.

preprint2011arXiv

Polar Patterns in Active Fluids

We study the spatio-temporal dynamics of a model of polar active fluid in two dimensions. The system exhibits a transition from an isotropic to a polarized state as a function of density. The uniform polarized state is, however, unstable above a critical value of activity. Upon increasing activity, the active fluids displays increasingly complex patterns, including traveling bands, traveling vortices and chaotic behavior. The advection arising from the particles self-propulsion and unique to polar fluids yields qualitatively new behavior as compared to that obtain in active nematic, with traveling-wave structures. We show that the nonlinear hydrodynamic equations can be mapped onto a simplified diffusion-reaction-convection model, highlighting the connection between the complex dynamics of active system and that of excitable systems.

preprint2010arXiv

Paraboloidal Crystals

The interplay between order and geometry in soft condensed matter systems is an active field with many striking results and even more open problems. Ordered structures on curved surfaces appear in multi-electron helium bubbles, viral and bacteriophage protein capsids, colloidal self-assembly at interfaces and in physical membranes. Spatial curvature can lead to novel ground state configurations featuring arrays of topological defects that would be excited states in planar systems. We illustrate this with a sequence of images showing the Voronoi lattice (in gold) and the corresponding Delaunay triangulations (in green) for ten low energy configurations of a system of classical charges constrained to lie on the surface of a paraboloid and interacting with a Coulomb potential. The parabolic geometry is considered as a specific realization of the class of crystalline structures on two-dimensional Riemannian manifolds with variable Gaussian curvature and boundary.

preprint2010arXiv

Sheared active fluids: thickening, thinning and vanishing viscosity

We analyze the behavior of a suspension of active polar particles under shear. In the absence of external forces, orientationally ordered active particles are known to exhibit a transition to a state of non-uniform polarization and spontaneous flow. Such a transition results from the interplay between elastic stresses, due to the liquid crystallinity of the suspension, and internal active stresses. In the presence of an external shear we find an extremely rich variety of phenomena, including an effective reduction (increase) in the apparent viscosity depending on the nature of the active stresses and the flow-alignment property of the particles, as well as more exotic behaviors such as a non-monotonic stress/strain-rate relation and yield stress for large activities.