arXiv subjects

François Graner

Publications and source records attributed to François Graner.

At least 19 recordsLinked to original sources

arXiv2026

Inference uncertainty about an aircraft crash

Problem-based learning benefits from situations taken from real life, which usually stimulate student interest. In this paper, we examine the shooting down of the Rwandan president's aircraft on April 6th, 1994. We discuss methods to infer information about the location from which the missile was launched, its trajectory and type, where the aircraft was struck and its trajectory during the fall. To this end, we developed a physics-based analysis based on expert reports, witness statements, and other publicly available information, as interpreted by our calculations. The analysis is designed to be understandable using undergraduate-level physics. The uncertainty of each result is discussed and propagated to ensure a proper assessment of the hypotheses and a traceability of their consequences. Such approach encourages the students to exercise their critical mind and teaches inference methods that are routinely used in physics research. In addition, it illustrates the importance and limits of scientific expertise during a judiciary process.

physics.ed-ph↗

arXiv2026

Benchmarking the flow of epithelial cell monolayer with self-aligning deformable active membranes

Collective cell migration emerges from the interplay between motility, deformability and mechanical interactions, yet incorporating these ingredients into computationally efficient tissue models remains challenging. Here, we benchmark self-aligning deformable active membranes in a confined-flow geometry that mimics epithelial monolayer migration around a circular obstacle. In this model, cells are represented as deformable, adhesive membranes whose self-propulsion direction relaxes towards their velocity. By systematically varying the self-alignment timescale, cell-cell adhesion and inlet forcing, we characterize the resulting flows through collective alignment, relative density, neighbor rearrangements and spatial velocity fields. The model captures a broad spectrum of tissue behaviors, ranging from disordered, liquid-like flows to highly aligned, solid-like states. Compared with a related multiparticle model, self-aligning active membranes achieve stronger collective alignment, exhibit a more systematic density response and access states closer to both limits of the solid-liquid spectrum. We further show that increasing the target shape index promotes cell elongation and accelerates tissue flow, directly linking cell-scale deformability to tissue-scale transport. Finally, we compare simulated velocity profiles with experimental measurements from in vitro migrating MDCK epithelial cell monolayers and find qualitative agreement across multiple horizontal and vertical transects around the obstacle. These results establish self-aligning deformable active membranes as a versatile framework for connecting cell mechanics, shape adaptation and self-alignment to collective tissue migration in confined geometries.

cond-mat.soft↗

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↗

arXiv2025

The Physics of Sustainability: Material and Power Constraints for the Long Term

Much of today's sustainability discourse emphasizes efficiency, clean technologies, and smart systems, but largely underestimates fundamental physical constraints relating to energy-matter interactions. These constraints stem from the fact that Earth is a materially closed yet energetically open system, driven by the sustained but low power-density flux of solar radiation. This Perspective reframes sustainability within these axiomatic limits, integrating relevant timescales and orders of magnitude. We argue that fossil-fueled industrial metabolism is inherently incompatible with long-term viability, while post-fossil systems are surface-, materials-, and power-intensive. Long-term sustainability must therefore be defined not only by how much energy or material is used, but also by how it is used: favoring organic, carbon-based chemistry with limited reliance on purified metals, operating at low power density, and maintaining low throughput rates. Achieving this requires radical technological shifts toward life-compatible systems and biogeochemical circular processes, and, likely as a consequence, a paradigm change toward degrowth to a steady-state. These two shifts are mutually reinforcing and together provide the necessary foundation for any viable future.

physics.soc-ph↗

arXiv2025

Geometric Confinement Reveals Scale-Free Velocity Correlations in Epithelial Cell Monolayer

Collective cell flows are a hallmark of tissue dynamics in development, wound healing, and various diseases. Here, we perform experiments on epithelial MDCK cell monolayers, over tens of hours without jamming, on millimeter-scale micropatterned substrates with or without free front (a strip or a closed racetrack). During maturation in time, domains and long-range correlations of the velocity field appear. Enstrophy increases (along with kinetic energy) during 5 hours, then passes through a maximum and decreases. Spatial velocity correlations are scale-free, following a power law, which challenges the notion of a single intrinsic correlation length. It suggests that the monolayer behaves as a critical-like system where information is transmitted across its entire size, a feature consistent with models of active solids capable of long-range stress propagation. The spatial correlation exponent significantly evolves with time, probably reflecting the monolayer maturation. The size, shape, topology and rigidity of patterned substrate influence the organization of flows and mechanical fields. Spontaneous collective motions are stronger on soft than on hard substrate. The presence of a free front accumulates vimentin on a much larger length scale than a fixed boundary ($65\pm 4$~$μ$m vs $3.2 \pm 0.7$~$μ$m), possibly revealing an underlying polarizing cue on the cell velocity field.

q-bio.TO↗

arXiv2023

Discriminating between individual-based models of collective cell motion in a benchmark flow geometry using standardised spatiotemporal patterns

Collectively coordinated cell migration plays a role in tissue embryogenesis, cancer, homeostasis and healing. To study these processes, different cell-based modelling approaches have been developed, ranging from lattice-based cellular automata to lattice-free models that treat cells as point-like particles or extended detailed cell shape contours. In the spirit of what Osborne et al. [PLOS Computational Biology, (2017) 13, 1-34] did for cellular tissue structure simulation models, we here compare five simulation models of collective cell migration, chosen to be representative in increasing order of included detail. They are Vicsek-Grégoire particles, Szabó-like particles, self-propelled Voronoi model, cellular Potts model, and multiparticle cells, where each model includes cell motility. We examine how these models compare when applied to the same biological problem, and what differences in behaviour are due to different model assumptions and abstractions. For that purpose, we use a benchmark that discriminates between complex material flow models, and that can be experimentally approached using cell cultures: the flow within a channel around a circular obstacle, that is, the geometry Stokes used in his historical 1851 experiment. For each model we explain how to best implement it; vary cell density, attraction force and alignment interaction; draw the resulting maps of velocity, density and deformation fields; and eventually discuss its respective advantages and limitations. We thus provide a recommendation on how to select a model to answer a given question, and we examine whether models of motile particles and motile cells display similar collective effects.

cond-mat.soft↗

arXiv2021

Shape-velocity correlation defines polarization in migrating cell simulations

Cell migration plays essential roles in development, wound healing, diseases, and in the maintenance of a complex body. Experiments in collective cell migration generally measure quantities such as cell displacement and velocity. The observed short-time diffusion regime for mean square displacement in single-cell migration experiments on flat surfaces calls into question the definition of cell velocity and the measurement protocol. Theoretical results in stochastic modeling for single-cell migration have shown that this fast diffusive regime is explained by a white noise acting on displacement on the direction perpendicular to the migrating cell polarization axis (not on velocity). The prediction is that only the component of velocity parallel to the polarization axis is a well-defined quantity, with a robust measurement protocol. Here, we ask whether we can find a definition of a migrating-cell polarization that is able to predict the cell's subsequent displacement, based on measurements of its shape. Supported by experimental evidence that cell nucleus lags behind the cell center of mass in a migrating cell, we propose a robust parametrization for cell migration where the distance between cell nucleus and the cell's center of mass defines cell shape polarization. We tested the proposed methods by applying to a simulation model for three-dimensional cells performed in the CompuCell3D environment, previously shown to reproduce biological cells kinematics migrating on a flat surface.

physics.bio-ph↗

arXiv2021

An appeal for an open scientific debate about the proximal origin of SARS-CoV-2

One year after the onset of the COVID-19 pandemic, the origin of SARS-CoV-2 still eludes humanity. Early publications firmly stated that the virus was of natural origin, and the possibility that the virus might have escaped from a lab was discarded in most subsequent publications. However, based on a re-analysis of the initial arguments, highlighted by the current knowledge about the virus, we show that the natural origin is not supported by conclusive arguments, and that a lab origin cannot be formally discarded. We call for an opening of peer-reviewed journals to a rational, evidence-based and prejudice-free evaluation of all the reasonable hypotheses about the virus' origin. We advocate that this debate should take place in the columns of renowned scientific journals, rather than being left to social media and newspapers.

q-bio.OT↗

arXiv2017

Unified presentation of four fundamental inequalities

We suggest an unified presentation to teach fundamental constants to graduate students, by introducing four lower limits to observed phenomena. The reduced Planck constant $\hbar$ is the lowest classically definable action. The inverse of invariant speed, $s$, is the lowest observable slowness. The Planck time, $t_{\rm P}$, is the lowest observable time scale. The Boltzmann constant, $k$, determines the lowest coherent degree of freedom; we recall a Einstein criterion on the fluctuations of small thermal systems and show that it has far-reaching implications, such as demonstrating the relations between critical exponents. Each of these four fundamental limits enters in an inequality, which marks a horizon of the universe we can perceive. This compact presentation can resolve some difficulties encountered when trying to defining the epistemologic status of these constants, and emphasizes their useful role in shaping our intuitive vision of the universe.

physics.pop-ph↗

arXiv2016

Quasicrystalline three-dimensional foams

We present a numerical study of quasiperiodic foams, in which the bubbles are generated as duals of quasiperiodic Frank-Kasper phases. These foams are investigated as potential candidates to the celebrated Kelvin problem for the partition of three-dimensional space with equal volume bubbles and minimal surface area. Interestingly, one of the computed structures falls close (but still slightly above) the best known Weaire-Phelan periodic candidate. This gives additional clues to understanding the main geometrical ingredients driving the Kelvin problem.

cond-mat.soft↗

arXiv2015

3D simulations of wet foam coarsening evidence a self similar growth regime

In wet liquid foams, slow diffusion of gas through bubble walls changes bubble pressure, volume and wall curvature. Large bubbles grow at the expenses of smaller ones. The smaller the bubble, the faster it shrinks. As the number of bubbles in a given volume decreases in time, the average bubble size increases: i.e. the foam coarsens. During coarsening, bubbles also move relative to each other, changing bubble topology and shape, while liquid moves within the regions separating the bubbles. Analyzing the combined effects of these mechanisms requires examining a volume with enough bubbles to provide appropriate statistics throughout coarsening. Using a Cellular Potts model, we simulate these mechanisms during the evolution of three-dimensional foams with wetnesses of $ϕ=0.00$, $0.05$ and $ 0.20$. We represent the liquid phase as an ensemble of many small fluid particles, which allows us to monitor liquid flow in the region between bubbles. The simulations begin with $2 \times 10^5$ bubbles for $ϕ= 0.00$ and $1.25 \times 10^5$ bubbles for $ϕ= 0.05$ and $0.20$, allowing us to track the distribution functions for bubble size, topology and growth rate over two and a half decades of volume change. All simulations eventually reach a self-similar growth regime, with the distribution functions time independent and the number of bubbles decreasing with time as a power law whose exponent depends on the wetness.

cond-mat.soft↗

arXiv2010

Discrete rearranging disordered patterns: Prediction of elastic and plastic behaviour, and application to two-dimensional foams

We study the elasto-plastic behaviour of materials made of individual (discrete) objects, such as a liquid foam made of bubbles. The evolution of positions and mutual arrangements of individual objects is taken into account through statistical quantities, such as the elastic strain of the structure, the yield strain and the yield function. The past history of the sample plays no explicit role, except through its effect on these statistical quantities. They suffice to relate the discrete scale with the collective, global scale. At this global scale, the material behaves as a continuous medium; it is described with tensors such as elastic strain, stress and velocity gradient. We write the differential equations which predict their elastic and plastic behaviour in both the general case and the case of simple shear. An overshoot in the shear strain or shear stress is interpreted as a rotation of the deformed structure, which is a purely tensorial effect that exists only if the yield strain is at least of order 0.3. We suggest practical applications, including: when to choose a scalar formalism rather than a tensorial one; how to relax trapped stresses; and how to model materials with a low, or a high, yield strain.

cond-mat.soft↗

arXiv2008

Screening in two-dimensional foams

Using the Surface Evolver software, we perform numerical simulations of point-like deformations in a two-dimensional foam. We study perturbations which are infinitesimal or finite, isotropic or anisotropic, and we either conserve or do not conserve the number of bubbles. We measure the displacement fields around the perturbation. Changes in pressure decrease exponentially with the distance to perturbation, indicating a screening over a few bubble diameters.

cond-mat.soft↗

arXiv2008

Topological and geometrical disorder correlate robustly in two-dimensional foams

A 2D foam can be characterised by its distribution of bubble areas, and of number of sides. Both distributions have an average and a width (standard deviation). There are therefore at least two very different ways to characterise the disorder. The former is a geometrical measurement, while the latter is purely topological. We discuss the common points and differences between both quantities. We measure them in a foam which is sheared, so that bubbles move past each other and the foam is "shuffled" (a notion we discuss). Both quantities are strongly correlated; in this case (only) it thus becomes sufficient to use either one or the other to characterize the foam disorder. We suggest applications to the analysis of other systems, including biological tissues.

cond-mat.soft↗

arXiv2008

Discrete rearranging disordered patterns, part II: 2D plasticity, elasticity and flow of a foam

The plastic flow of a foam results from bubble rearrangements. We study their occurrence in experiments where a foam is forced to flow in 2D: around an obstacle; through a narrow hole; or sheared between rotating disks. We describe their orientation and frequency using a topological matrix defined in the companion paper (Graner et al., preprint), which links them with continuous plasticity at large scale. We then suggest a phenomenological equation to predict the plastic strain rate: its orientation is determined from the foam's local elastic strain; and its rate is determined from the foam's local elongation rate. We obtain a good agreement with statistical measurements. This enables us to describe the foam as a continuous medium with fluid, elastic and plastic properties. We derive its constitutive equation, then test several of its terms and predictions.

cond-mat.soft↗

arXiv2008

Discrete rearranging disordered patterns, part I: Robust statistical tools in two or three dimensions

Discrete rearranging patterns include cellular patterns, for instance liquid foams, biological tissues, grains in polycrystals; assemblies of particles such as beads, granular materials, colloids, molecules, atoms; and interconnected networks. Such a pattern can be described as a list of links between neighbouring sites. Performing statistics on the links between neighbouring sites yields average quantities (hereafter "tools") as the result of direct measurements on images. These descriptive tools are flexible and suitable for various problems where quantitative measurements are required, whether in two or in three dimensions. Here, we present a coherent set of robust tools, in three steps. First, we revisit the definitions of three existing tools based on the texture matrix. Second, thanks to their more general definition, we embed these three tools in a self-consistent formalism, which includes three additional ones. Third, we show that the six tools together provide a direct correspondence between a small scale, where they quantify the discrete pattern's local distortion and rearrangements, and a large scale, where they help describe a material as a continuous medium. This enables to formulate elastic, plastic, fluid behaviours in a common, self-consistent modelling using continuous mechanics. Experiments, simulations and models can be expressed in the same language and directly compared. As an example, a companion paper (Marmottant, Raufaste and Graner, joint paper) provides an application to foam plasticity.

cond-mat.soft↗

arXiv2007

Cell adhesion and cortex contractility determine cell patterning in the Drosophila retina

Hayashi and Carthew (Nature 431 [2004], 647) have shown that the packing of cone cells in the Drosophila retina resembles soap bubble packing, and that changing E- and N-cadherin expression can change this packing, as well as cell shape. The analogy with bubbles suggests that cell packing is driven by surface minimization. We find that this assumption is insufficient to model the experimentally observed shapes and packing of the cells based on their cadherin expression. We then consider a model in which adhesion leads to a surface increase, balanced by cell cortex contraction. Using the experimentally observed distributions of E- and N-cadherin, we simulate the packing and cell shapes in the wildtype eye. Furthermore, by changing only the corresponding parameters, this model can describe the mutants with different numbers of cells, or changes in cadherin expression.

q-bio.CB↗

arXiv2007

Yield drag in a two-dimensional foam flow around a circular obstacle: Effect of liquid fraction

We study the two-dimensional flow of foams around a circular obstacle within a long channel. In experiments, we confine the foam between liquid and glass surfaces. In simulations, we use a deterministic software, the Surface Evolver, for bubble details and a stochastic one, the extended Potts model, for statistics. We adopt a coherent definition of liquid fraction for all studied systems. We vary it in both experiments and simulations, and determine the yield drag of the foam, that is, the force exerted on the obstacle by the foam flowing at very low velocity. We find that the yield drag is linear over a large range of the ratio of obstacle to bubble size, and is independent of the channel width over a large range. Decreasing the liquid fraction, however, strongly increases the yield drag; we discuss and interpret this dependence.

cond-mat.soft↗