arXiv subjects

Jean-Francois Joanny

Publications and source records attributed to Jean-Francois Joanny.

At least 19 recordsLinked to original sources

arXiv2026

Hydrodynamic theory of chemically active emulsions

We present a systematic theory of chemically active emulsions in the hydrodynamic limit by constructing a thermodynamically consistent framework in which the equilibrium is broken by chemo-stating of fuel molecules. For ternary solutions with active chemical reactions, we obtain an effective dynamics of the conserved field dynamics at long length and time scales. The effective dynamics takes into account the broken time reversal symmetry that manifests itself by the emergence of gradient terms akin to those of Active Model B+, which is a generic theory of active phase separation. In addition to the active coefficients modifying the interfacial energy coefficient, the theory contains higher order terms in the gradient expansion that are necessary to correctly describe the dynamics of chemically active emulsions, extending thus Active Model B+. We study numerically a Flory-Huggins model with active chemical reactions. Our theory predicts the formation of microphases when the effective interfacial energy coefficient becomes negative. Moreover, including noise, we show the existence of bubbly phase separation. We also identify a new type of phase behavior, a dynamic active filament phase. Finally, we discuss the steady state entropy production rate in the system resulting from the active chemical reactions. We observe that the total entropy production rate increases with the driving chemical potential and exhibits a kink-like singularity at the transition to the dynamic active filament phase. Our work shows that the generic behaviors of active phase separation can emerge in chemically active emulsions.

cond-mat.soft↗

arXiv2026

Phase separation by polar active transport

We propose an active Cahn-Hilliard theory for the dynamics of a new type of phase transition where the driving force is not the direct interactions between the two separating components, but their active sorting by a third polar species. This third species can transport the other two along its polarity in opposite directions, thus separating them. Inspired by recent experiments where molecular motors that walk in opposite directions along microtubules are sorted into separated domains, our theoretical description of this process introduces a new mechanism for active phase separation and could serve as a model for the organization of biological material in space inside cells. We predict the formation of motor domains, and further show that they can either coarsen to form macroscopic phases or reach a finite micro- or mesoscopic steady state size, these latter due to an arrest of coarsening through activity.

cond-mat.soft↗

arXiv2023

Rheology of 2D vertex model

The mechanical properties of tissues play an essential role for all tissue properties such as cell division, and differentiation or morphogenesis. Here, we study theoretically the rheology of 2-dimensional epithelial tissues described by a discrete vertex-like model, using an analytical coarsegrained continuum formulation. We show that epithelial tissues are most often shear-thinning under constant shear rate, and in certain circumstances cross over from shear thickening at low shear rates to shear thinning at high shear rates. We give an analytical expression of the tissue response in an oscillating strain experiment in the linear regime, and calculate it numerically in the non-linear regime. When the tissue is supported by an oscillating substrate, it reorients depending on frequency and substrate's Poisson's ratio. Reorientation could be gradual or abrupt, depending on tissue and substrate parameters, and the configuration phase space exhibits a tricritical point.

cond-mat.soft↗

arXiv2021

Instabilities and geometry of growing tissues

We derive a course grained, continuum model of the 2D vertex model, applicable for different underlying geometries, and allowing for analytical analysis of an otherwise numerical model. Using a geometric approach and out--of--equilibrium statistical mechanics, we calculate both mechanical and dynamical instabilities within a tissue, and their dependence on different variables, including activity, and disorder. Most notably, the tissue's response depends on the existence of mechanical residual stresses in the tissue. Thus, even freely growing tissues may exhibit a growth instability depending on food consumption. Using this geometric model we can readily distinct between elasticity and plasticity in a growing, flowing, tissue.

cond-mat.soft↗

arXiv2020

Vertex model instabilities for tissues subject to cellular activity or applied stresses

The vertex model is widely used to describe the dynamics of epithelial tissues, because of its simplicity and versatility and the direct inclusion of biophysical parameters. Here, it is shown that quite generally, when cells modify their equilibrium perimeter due to their activity, or the tissue is subject to external stresses, the tissue becomes unstable with deformations that couple pure-shear or deviatoric modes, with rotation and expansion modes. For short times, these instabilities deform cells increasing their ellipticity while, at longer times, cells become non-convex, indicating that the vertex model ceases to be a valid description for tissues under these conditions. The agreement between the analytic calculations performed for a regular hexagonal tissue and the simulations of disordered tissues is excellent due to the homogenization of the tissue at long wavelengths.

cond-mat.soft↗

arXiv2019

Casimir stresses in active nematic films

We calculate the Casimir stresses in a thin layer of active fluid with nematic order. By using a stochastic hydrodynamic approach for an active fluid layer of finite thickness $L$, we generalize the Casimir stress for nematic liquid crystals in thermal equilibrium to active systems. We show that the active Casimir stress differs significantly from its equilibrium counterpart. For contractile activity, the active Casimir stress, although attractive like its equilibrium counterpart, diverges logarithmically as $L$ approaches a threshold of the spontaneous flow instability from below. In contrast, for small extensile activity, it is repulsive, has no divergence at any $L$ and has a scaling with $L$ different from its equilibrium counterpart.

cond-mat.soft↗

arXiv2013

The actin cortex as an active wetting layer

Using active gel theory we study theoretically the properties of the cortical actin layer of animal cells. The cortical layer is described as a non-equilibrium wetting film on the cell membrane. The actin density is approximately constant in the layer and jumps to zero at its edge. The layer thickness is determined by the ratio of the polymerization velocity and the depolymerization rate of actin.

cond-mat.soft↗

arXiv2012

Mechanical Instabilities of Biological Tubes

We study theoretically the shapes of biological tubes affected by various pathologies. When epithelial cells grow at an uncontrolled rate, the negative tension produced by their division provokes a buckling instability. Several shapes are investigated : varicose, enlarged, sinusoidal or sausage-like, all of which are found in pathologies of tracheal, renal tubes or arteries. The final shape depends crucially on the mechanical parameters of the tissues : Young modulus, wall-to-lumen ratio, homeostatic pressure. We argue that since tissues must be in quasistatic mechanical equilibrium, abnormal shapes convey information as to what causes the pathology. We calculate a phase diagram of tubular instabilities which could be a helpful guide for investigating the underlying genetic regulation.

physics.bio-ph↗

arXiv2012

Instabilities of monolayered epithelia: shape and structure of villi and crypts

We study theoretically the shapes of a dividing epithelial monolayer of cells lying on top of an elastic stroma. The negative tension created by cell division provokes a buckling instability at a finite wave vector leading to the formation of periodic arrays of villi and crypts. The instability is similar to the buckling of a metallic plate under compression. We use the results to rationalize the various structures of the intestinal lining observed \emph{in vivo}. Taking into account the coupling between cell division and local curvature, we obtain different patterns of villi and crypts, which could explain the different morphologies of the small intestine and the colon.

physics.bio-ph↗

arXiv2012

A Drop of Active Matter

We study theoretically the hydrodynamics of a fluid drop containing oriented filaments endowed with active contractile or extensile stresses and placed on a solid surface. The active stresses alter qualitatively the wetting properties of the drop, leading to new spreading laws and novel static drop shapes. Candidate systems for testing our predictions include cytoskeletal extracts with motors and ATP, suspensions of bacteria or pulsatile cells, or fluids laden with artificial self-propelled colloids.

cond-mat.soft↗

arXiv2011

Undulation Instability of Epithelial Tissues

Treating the epithelium as an incompressible fluid adjacent to a viscoelastic stroma, we find a novel hydrodynamic instability that leads to the formation of protrusions of the epithelium into the stroma. This instability is a candidate for epithelial fingering observed in vivo. It occurs for sufficiently large viscosity, cell-division rate and thickness of the dividing region in the epithelium. Our work provides physical insight into a potential mechanism by which interfaces between epithelia and stromas undulate, and potentially by which tissue dysplasia leads to cancerous invasion.

physics.bio-ph↗

arXiv2010

Role of ATP-hydrolysis in the dynamics of a single actin filament

We study the stochastic dynamics of growth and shrinkage of single actin filaments taking into account insertion, removal, and ATP hydrolysis of subunits either according to the vectorial mechanism or to the random mechanism. In a previous work, we developed a model for a single actin or microtubule filament where hydrolysis occurred according to the vectorial mechanism: the filament could grow only from one end, and was in contact with a reservoir of monomers. Here we extend this approach in several ways, by including the dynamics of both ends and by comparing two possible mechanisms of ATP hydrolysis. Our emphasis is mainly on two possible limiting models for the mechanism of hydrolysis within a single filament, namely the vectorial or the random model. We propose a set of experiments to test the nature of the precise mechanism of hydrolysis within actin filaments.

q-bio.BM↗

arXiv2009

Homeostatic competition drives tumor growth and metastasis nucleation

We propose a mechanism for tumor growth emphasizing the role of homeostatic regulation and tissue stability. We show that competition between surface and bulk effects leads to the existence of a critical size that must be overcome by metastases to reach macroscopic sizes. This property can qualitatively explain the observed size distributions of metastases, while size-independent growth rates cannot account for clinical and experimental data. In addition, it potentially explains the observed preferential growth of metastases on tissue surfaces and membranes such as the pleural and peritoneal layers, suggests a mechanism underlying the seed and soil hypothesis introduced by Stephen Paget in 1889 and yields realistic values for metastatic inefficiency. We propose a number of key experiments to test these concepts. The homeostatic pressure as introduced in this work could constitute a quantitative, experimentally accessible measure for the metastatic potential of early malignant growths.

q-bio.TO↗

arXiv2008

Non-equilibrium self-assembly of a filament coupled to ATP/GTP hydrolysis

We study the stochastic dynamics of growth and shrinkage of single actin filaments or microtubules taking into account insertion, removal, and ATP/GTP hydrolysis of subunits. The resulting phase diagram contains three different phases: a rapidly growing phase, an intermediate phase and a bound phase. We analyze all these phases, with an emphasis on the bound phase. We also discuss how hydrolysis affects force-velocity curves. The bound phase shows features of dynamic instability, which we characterize in terms of the time needed for the ATP/GTP cap to disappear as well as the time needed for the filament to reach a length of zero, i.e., (to collapse) for the first time. We obtain exact expressions for all these quantities, which we test using Monte Carlo simulations.

cond-mat.soft↗

arXiv2005

Theoretical Study of Comb-Polymers Adsorption on Solid Surfaces

We propose a theoretical investigation of the physical adsorption of neutral comb-polymers with an adsorbing skeleton and non-adsorbing side-chains on a flat surface. Such polymers are particularly interesting as "dynamic coating" matrices for bio-separations, especially for DNA sequencing, capillary electrophoresis and lab-on-chips. Separation performances are increased by coating the inner surface of the capillaries with neutral polymers. This method allows to screen the surface charges, thus to prevent electro-osmosis flow and adhesion of charged macromolecules (e.g. proteins) on the capillary walls. We identify three adsorption regimes: a "mushroom" regime, in which the coating is formed by strongly adsorbed skeleton loops and the side-chains anchored on the skeleton are in a swollen state, a "brush" regime, characterized by a uniform multi-chains coating with an extended layer of non-adsorbing side-chains and a non-adsorbed regime. By using a combination of mean field and scaling approaches, we explicitly derive asymptotic forms for the monomer concentration profiles, for the adsorption free energy and for the thickness of the adsorbed layer as a function of the skeleton and side-chains sizes and of the adsorption parameters. Moreover, we obtain the scaling laws for the transitions between the different regimes. These predictions can be checked by performing experiments aimed at investigating polymer adsorption, such as Neutron or X-ray Reflectometry, Ellipsometry, Quartz Microbalance, or Surface Force Apparatus.

cond-mat.soft↗

arXiv2004

Fission of a multiphase membrane tube

A common mechanism for intracellular transport is the use of controlled deformations of the membrane to create spherical or tubular buds. While the basic physical properties of homogeneous membranes are relatively well-known, the effects of inhomogeneities within membranes are very much an active field of study. Membrane domains enriched in certain lipids in particular are attracting much attention, and in this Letter we investigate the effect of such domains on the shape and fate of membrane tubes. Recent experiments have demonstrated that forced lipid phase separation can trigger tube fission, and we demonstrate how this can be understood purely from the difference in elastic constants between the domains. Moreover, the proposed model predicts timescales for fission that agree well with experimental findings.

physics.bio-ph↗

arXiv2004

Generic theory of active polar gels: a paradigm for cytoskeletal dynamics

We develop a general theory for active viscoelastic materials made of polar filaments. This theory is motivated by the dynamics of the cytoskeleton. The continuous consumption of a fuel generates a non equilibrium state characterized by the generation of flows and stresses. Our theory can be applied to experiments in which cytoskeletal patterns are set in motion by active processes such as those which are at work in cells.

physics.bio-ph↗

arXiv2004

Fast DNA translocation through a solid-state nanopore

We report translocation experiments on double-strand DNA through a silicon oxide nanopore. Samples containing DNA fragments with seven different lengths between 2000 to 96000 basepairs have been electrophoretically driven through a 10 nm pore. We find a power-law scaling of the translocation time versus length, with an exponent of 1.26 $\pm$ 0.07. This behavior is qualitatively different from the linear behavior observed in similar experiments performed with protein pores. We address the observed nonlinear scaling in a theoretical model that describes experiments where hydrodynamic drag on the section of the polymer outside the pore is the dominant force counteracting the driving. We show that this is the case in our experiments and derive a power-law scaling with an exponent of 1.18, in excellent agreement with our data.

q-bio.BM↗