arXiv subjects

Philippe Peyla

Publications and source records attributed to Philippe Peyla.

17 recordsLinked to original sources

arXiv2026

Geometry-Controlled Motility of Microswimmers in elementary microfluidic confinements

The motility of microswimmers in confined environments is a fundamental problem in active matter physics, with direct implications for microfluidic applications and the understanding of microorganism behavior in complex natural habitats. Although the run-and-tumble dynamics of flagellated microalgae such as Chlamydomonas Reinhardtii (CR) are well characterized in bulk suspension, the extent to which elementary geometric confinements alter their swimming remains insufficiently understood, particularly regarding the relative contributions of steric contact versus hydrodynamic interactions. Here, we experimentally investigate the trajectories of individual CR cells in a diversity of PDMS microfluidic geometries of growing complexity using single-particle tracking and statistical analysis. We show that cells in straight channels accumulate near walls and align along the channel axis, a behavior qualitatively reproduced by steric Active Brownian Particle simulations, yet showing a confinement-dependent velocity enhancement consistent with hydrodynamic wall coupling. In circular cavities with diameter below the persistence length L_0 ~350 microns, cells transition from bulk active Brownian exploration to quasi-circular wall-following trajectories. In dumbbell geometries, inter-compartment dwell length reflect purely geometric predictions, evidencing no measurable hydrodynamic contributions even for strong confinements. Together, these results demonstrate that environmental geometry can selectively amplify or suppress motility modes in active biological suspensions, opening avenues for the passive control of microswimmer transport in engineered microfluidic networks.

cond-mat.soft↗

arXiv2024

Universal Scaling Laws for a Generic Swimmer Model

We have developed a minimal model of a swimmer without body deformation based on force and torque dipoles which allows accurate 3D Navier-Stokes calculations. Our model can reproduce swimmer propulsion for a large range of Reynolds numbers, and generate wake vortices in the inertial regime, reminiscent of the flow generated by the flapping tails of real fish. We performed a numerical exploration of the model from low to high Reynolds numbers and obtained universal laws using scaling arguments. We collected data from a wide variety of micro-organisms, thereby extending the experimental data presented in (M. Gazzola et al., Nature Physics 10, 758, 2014). Our theoretical scaling laws compare very well with experimental data across the different regimes, from Stokes to turbulent flows. We believe that this model, due to its relatively simple design, will be very useful for obtaining numerical simulations of collective effects within fish schools composed of hundreds of individuals.

physics.bio-ph↗

arXiv2024

Behavioral transition of a fish school in a crowded environment

In open water, social fish gather to form schools, in which fish generally align with each other. In this work, we study how this social behavior evolves when perturbed by artificial obstacles. We measure the collective behavior of a group of zebrafish in the presence of a periodic array of pillars. When pillar density is low, the fish regroup with a typical inter-distance and a well-polarized state with parallel orientations, similar to their behavior in open water conditions. Above a critical density of pillars, their social interactions, which are mostly based on vision, are screened and the fish spread randomly through the aquarium, orienting themselves along the free axes of the pillar lattice. The abrupt transition from natural to artificial orientation happens when the pillar inter-distance is comparable to the social distance of the fish, i.e., their most probable inter-distance. We develop a stochastic model of the relative orientation between fish pairs, taking into account alignment, anti-alignment and tumbling, from a distribution biased by the environment. This model provides a good description of the experimental probability distribution of the relative orientation between the fish and captures the behavioral transition. Using the model to fit the experimental data provides qualitative information on the evolution of cognitive parameters, such as the alignment or the tumbling rates, as the pillar density increases. At high pillar density, we find that the artificial environment imposes its geometrical constraints to the fish school, drastically increasing the tumbling rate.

physics.bio-ph↗

arXiv2020

Collective orientation of an immobile fish school, effect on rheotaxis

We study the orientational order of an immobile fish school. Starting from the second Newton's law, we show that the inertial dynamics of orientations is ruled by an Ornstein-Uhlenbeck process. This process describes the dynamics of alignment between neighboring fish in a shoal, a dynamics already used in the literature for mobile fish schools. Firstly, in a fluid at rest, we calculate the global polarization (i.e. the mean orientation of the fish) which decreases rapidly as a function of the noise. We show that the faster a fish is able to reorient itself, the more the school can afford to reorder itself for important noise values. Secondly, in the prescence of a stream, each fish tends to orient itself and swims against the flow: the so-called rheotaxis. So even in the presence of a flow, it results in an immobile fish school. By adding an individual rheotaxis effect to alignment interaction between fish, we show that in a noisy environment, individual rheotaxis is enhanced by alignment interactions between fish.

physics.bio-ph↗

arXiv2020

Deflection of phototactic microswimmers through obstacle arrays

We study the effect of inhomogeneous environments on the swimming direction of the microalgae \textit{Chlamydomonas Reinhardtii} (CR) in the presence of a light stimulus. Positive or negative phototaxis describe the ability of microorganisms to bias their swimming towards or away from a light source. Here we consider microswimmers with negative phototaxis in a microfluidic device with a microfabricated square lattice of pillars as obstacles. We measured a mean deflection of microswimmers that shows an interesting nonlinear dependence on the direction of the guiding light beam with respect to the symmetry axes of the pillar lattice. By simulating a model swimmer in a pillar lattice and analyzing its scattering behavior, we identified the width of the reorientation distribution of swimmers to be also crucial for the nonlinear behavior of the swimmer deflection. On the basis of these results we suggest in addition an analytical model for microswimmers, where the pillar lattice is replaced by an anisotropic scattering medium, that depends only on a scattering rate and the width of the reorientation distribution of swimmers. This flexible and handy model fits the experimental results as well. The presented analysis of the deflection of light guided swimmers through pillar lattice may be used for separating swimmers having different reorientation distributions.

cond-mat.soft↗

arXiv2020

Extreme congestion of microswimmers at a bottleneck constriction

When attracted by a stimulus (e. g. light), microswimmers can build up very densely at a constriction and thus cause clogging. The micro-alga \textit{Chlamydomonas Reinhardtii} is used here as a model system to study this phenomenon. Its negative phototaxis makes the algae swim away from a light source and go through a microfabricated bottleneck-shaped constriction. Successive clogging events interspersed with bursts of algae are observed. A power law decrease is found to describe well the distribution of time lapses of blockages. Moreover, the evacuation time is found to increase when increasing the swimming velocity. These results might be related to the phenomenology of crowd dynamics and in particular what has been called the Faster is Slower effect in the dedicated literature. It also raises the question of the presence of tangential solid friction between motile cells densely packed that may accompany arches formation. Using the framework of crowd dynamics we analyze the microswimmers behavior and in particular question the role of hydrodynamics.

cond-mat.soft↗

arXiv2018

Effective diffusivity of microswimmers in a crowded environment

The microalga Chlamydomonas Reinhardtii (CR) is used here as a model system to study the effect of complex environments on the swimming of micro-organisms. Its motion can be modelled by a run and tumble mechanism so that it describes a persistent random walk from which we can extract an effective diffusion coefficient for the large-time dynamics. In our experiments, the complex medium consists in a series of pillars that are designed in a regular lattice using soft lithography microfabrication. The cells are then introduced in the lattice, and their trajectories within the pillars are tracked and analyzed. The effect of the complex medium on the swimming behaviour of microswimmers is analyzed through the measure of relevant statistical observables. In particular, the mean correlation time of direction and the effective diffusion coefficient are shown to decrease when increasing the density of pillars. This provides some bases of understanding for active matter in complex environments.

cond-mat.soft↗

arXiv2017

Effective viscosity of a suspension of flagellar beating microswimmers: Three-dimensional modeling

Micro-organisms usually can swim in their liquid environment by flagellar or ciliary beating. In this numerical work, we analyze the influence of flagellar beating on the orbits of a swimming cell in a shear flow. We also calculate the effect of the flagellar beating on the rheology of a dilute suspension of micro-swimmers. A three-dimensional model is proposed for Chlamydomonas Reinhardtii swimming with a breaststroke-like beating of two anterior flagella modeled by two counter-rotating fore beads. The active swimmer model reveals unusual angular orbits in a linear shear flow. Namely, the swimmer sustains orientations transiently across the flow. Such behavior is a result of the interplay between shear flow and swimmer's periodic beating motion of flagella which exert internal torques on the cell body. This peculiar behavior has some significant consequences on the rheological properties of the suspension. We calculate the Einstein's viscosity of the suspension composed of such isolated modeled microswimmers (dilute case) in a shear flow. We use numerical simulations based on a Rotne-Prager like approximation for hydrodynamic interaction between simplified flagella and the cell body. The results show an increased intrinsic viscosity for active swimmer suspensions in comparison to non-active ones as well as a shear thinning behavior in accordance with previous experimental measurements [Phys. Rev. Lett. 104 , 098102 (2010)].

cond-mat.soft↗

arXiv2016

Photofocusing: Light and flow of phototactic microswimmer suspension

We explore in this paper the phenomenon of photofocusing: a coupling between flow vorticity and biased swimming of microalgae toward a light source that produces a focusing of the microswimmer suspension. We combine experiments that investigate the stationary state of this phenomenon as well as the transition regime with analytical and numerical modeling. We show that the experimentally observed scalings on the width of the focalized region and the establishment length as a function of the flow velocity are well described by a simple theoretical model.

cond-mat.soft↗

arXiv2013

Effective viscosity of non-gravitactic Chlamydomonas Reinhardtii microswimmer suspensions

Active microswimmers are known to affect the macroscopic viscosity of suspensions in a more complex manner than passive particles. For puller-like microswimmers an increase in the viscosity has been observed. It has been suggested that the persistence of the orientation of the microswimmers hinders the rotation that is normally caused by the vorticity. It was previously shown that some sorts of algaes are bottom-heavy swimmers, i.e. their centre of mass is not located in the centre of the body. In this way, the algae affects the vorticity of the flow when it is perpendicular oriented to the axis of gravity. This orientation of gravity to vorticity is given in a rheometer that is equipped with a cone-plate geometry. Here we present measurements of the viscosity both in a cone-plate and a Taylor-Couette cell. The two set-ups yielded the same increase in viscosity although the axis of gravitation in the Taylor-Couette cell is parallel to the direction of vorticity. In a complementary experiment we tested the orientation of the direction of swimming through microscopic observation of single \textit{Chlamydomonas reinhardtii} and could not identify a preferred orientation, i. e. our specific strain of \textit{Chlamydomonas reinhardtii} are not bottom-heavy swimmers. We thus conclude that bottom heaviness is not a prerequisite for the increase of viscosity and that the effect of gravity on the rheology of our strain of \textit{Chlamydomonas reinhardtii} is negligible. This finding reopens the question of whether origin of persistence in the orientation of cells is actually responsible for the increased viscosity of the suspension.

physics.bio-ph↗

arXiv2013

Dumbbells in suspension: A numerical study on their dynamics and shear viscosity

The dynamics of elastic dumbbells in linear shear flow is investigated by fluid particle dynamics simulations at small Reynolds numbers. The positive contribution of a single dumbbell to the effective shear viscosity is determined via the extra stress exerted at the boundaries of the shear cell and the difference to the contributions obtained via the Kramers-Kirkwood formula are described. For a small Weissenberg number and when the mean dumbbell length becomes larger than the mean next-neighbor distance, the contribution of interacting dumbbells to the mean shear viscosity exceeds significantly the contribution of unconnected beads occupying the same volume fraction.

cond-mat.soft↗

arXiv2013

Wall attraction and repulsion of hydrodynamically interacting particles

We investigate hydrodynamic interaction effects between colloidal particles in the vicinity of a wall in the low Reynolds-number limit. Hydrodynamically interacting pairs of beads being dragged by a force parallel to a wall, as for instance during sedimentation, are repelled by the boundary. If a pair of beads is trapped by harmonic potentials parallel to the external flow and at the same distance to a wall, then the particle upstream is repelled from the boundary while its neighbor downstream is attracted. The free end of a semiflexible bead-spring polymer-model, which is fixed at one end in a flow near a wall, is bent towards the wall by the same reason. The results obtained for point-like particles are exemplarily confirmed by fluid particle dynamics simulations for beads of finite radii, where the shear induced particle rotations either weaken or enhance the the effects obtained for point-like particles.

cond-mat.soft↗

arXiv2013

Light control of the flow of phototactic microswimmer suspensions

Some micro-algae are sensitive to light intensity gradients. This property is known as phototaxis: the algae swim toward a light source (positive phototaxis). We use this property to control the motion of micro-algae within a Poiseuille flow using light. The combination of flow vorticity and phototaxis results in a concentration of algae around the center of the flow. Intermittent light exposure allows analysis of the dynamics of this phenomenon and its reversibility. With this phenomenon, we hope to pave the way toward new algae concentration techniques (a bottleneck challenge in hydrogen algal production) and toward the improvement of pollutant bio-detector technology.

cond-mat.soft↗

arXiv2011

The random walk of a low-Reynolds-number swimmer

Swimming at a micrometer scale demands particular strategies. Indeed when inertia is negligible as compared to viscous forces (i.e. Reynolds number $Re$ is lower than unity), hydrodynamics equations are reversible in time. To achieve propulsion at low Reynolds number, swimmers must then deform in a way that is not invariant under time reversal. Here, we investigate dispersal properties of self propelled organisms by means of microscopy and cell tracking. Our system of interest is the micro-alga \textit{Chlamydomonas Reinhardtii}, a motile single celled green alga about 10 micrometers in diameter that swims with to two front flagella. In the case of dilute suspensions, we show that tracked trajectories are well modeled by a correlated random walk. This process is based on short time correlations in the direction of movement called persistence. At longer times, correlations are lost and a standard random walk characterizes the trajectories. Moreover, high speed imaging enables us to show how the back-and-forth motion of flagella at very short times affects the statistical description of the dynamics. Finally we show how drag forces modify the characteristics of this particular random walk.

cond-mat.soft↗

arXiv2010

A constitutive law for cross-linked actin networks by homogenization techniques

Inspired by experiments on the actin driven propulsion of micrometer sized beads we develop and study a minimal mechanical model of a two-dimensional network of stiff elastic filaments grown from the surface of a cylinder. Starting out from a discrete model of the network structure and of its microscopic mechanical behavior we derive a macroscopic constitutive law by homogenization techniques. We calculate the axisymmetric equilibrium state and study its linear stability depending on the microscopic mechanical properties. We find that thin networks are linearly stable, whereas thick networks are unstable. The critical thickness for the change in stability depends on the ratio of the microscopic elastic constants. The instability is induced by the increase in the compressive load on the inner network layers as the thickness of the network increases. The here employed homogenization approach combined with more elaborate microscopic models can serve as a basis to study the evolution of polymerizing actin networks and the mechanism of actin driven motion.

cond-mat.soft↗

arXiv2010

Effective viscosity of microswimmer suspensions

The measurement of a quantitative and macroscopic parameter to estimate the global motility of a large population of swimming biological cells is a challenge Experiments on the rheology of active suspensions have been performed. Effective viscosity of sheared suspensions of live unicellular motile micro-algae (\textit{Chlamydomonas Reinhardtii}) is far greater than for suspensions containing the same volume fraction of dead cells and suspensions show shear thinning behaviour. We relate these macroscopic measurements to the orientation of individual swimming cells under flow and discuss our results in the light of several existing models.

cond-mat.soft↗

arXiv2009

Actin based propulsion: Intriguing interplay between material properties and growth processes

Eukaryotic cells and intracellular pathogens such as bacteria or viruses utilize the actin polymerization machinery to propel themselves forward. Thereby, the onset of motion and choice of direction may be the result of a spontaneous symmetry-breaking or might be triggered by external signals and preexisting asymmetries, e.g. through a previous septation in bacteria. Although very complex, a key feature of cellular motility is the ability of actin to form dense polymeric networks, whose microstructure is tightly regulated by the cell. These polar actin networks produce the forces necessary for propulsion but may also be at the origin of a spontaneous symmetry-breaking. Understanding the exact role of actin dynamics in cell motility requires multiscale approaches which capture at the same time the polymer network structure and dynamics on the scale of a few nanometers and the macroscopic distribution of elastic stresses on the scale of the whole cell. In this chapter we review a selection of theories on how mechanical material properties and growth processes interact to induce the onset of actin based motion.

cond-mat.soft↗