arXiv subjects

Carine Douarche

Publications and source records attributed to Carine Douarche.

13 recordsLinked to original sources

arXiv2026

Local chemotactic response of $Escherichia$ $coli$ in fluid and near surfaces

Bacteria can adjust their swimming behaviour in response to chemical variations, a phenomenon known as chemotaxis. This process is characterised by a drift velocity that depends non-linearly on the concentration of chemical species and its "local" gradient. To study this process more effectively, we optimised a 3-channel microfluidic device to generate a stable, linear concentration profile of chemoattractants. This setup allows us to monitor the response of $Escherichia$ $coli$ to casamino acids or $α$-methyl-DL-aspartic acid at the individual level. By analysing the movement of a population of individuals both in fluid and on surfaces, we achieve faster, more accurate quantification of the population's chemotactic response. In the fluid, the chemotactic response is described by the equation $v_c=χ(c) \nabla c$, with $χ(c) = χ_0 /[(1 + c/c_-)(1 + c/c_+)]$ the chemotactic susceptibility. For $c_- \ll c \ll c_+$, i.e. when bacteria perform chemotaxis, the bacterial chemotactic velocity is proportional to the concentration gradient divided by the concentration and $v_c \propto \nabla c/c = \nabla (\log c)$. However, on surfaces, the chemotactic flux is inhibited.

physics.flu-dyn↗

arXiv2026

Number fluctuations distinguish different self-propelling dynamics

In nonequilibrium suspensions, static number fluctuations $N$ in virtual observation boxes reveal remarkable structural properties, but the dynamic potential of $N(t)$ signals remains unexplored. Here, we develop a theory to learn the dynamical parameters of self-propelled particle models from $N(t)$ statistics. Unlike traditional trajectory analysis, $N(t)$ statistics distinguish between models, by sensing subtle differences in reorientation dynamics that govern re-entrance events in boxes. This paves the way for quantifying advanced dynamic features in dense nonequilibrium suspensions.

cond-mat.soft↗

arXiv2026

The Countoscope for self-propelled particles

Particle number fluctuations $N(t)$, measured in virtual observation boxes of an image or a simulation, offer a way to quantify particle dynamics when particle tracking is impractical, such as in high-density systems. While traditionally limited to equilibrium diffusive systems, we extend this approach -- named ``Countoscope'' -- to out-of-equilibrium self-propelled particles: Active Brownian (ABPs), Run and Tumble (RTPs), and Active Ornstein-Uhlenbeck Particles (AOUPs). For AOUPs, we leverage their Gaussian statistics to derive a general formula applicable to any Gaussian system. For ABPs and RTPs, we derive the intermediate scattering function (ISF) -- and thus the correlations of $N(t)$ -- using an exact perturbative expansion over the probability density fields, revealing key physical features of the ISF and of the number correlations. Our theoretical predictions for the mean-squared number difference $\langle ΔN^2(t) \rangle = \langle (N(t) - N(0))^2 \rangle$ match stochastic simulations and exhibit three time-dependent scaling regimes: diffusive, advective, and long-time enhanced diffusive, reflecting the regimes of the mean squared particle displacement. We further uncover limiting laws in each of these regimes that are useful to quantify self-propulsion properties.

cond-mat.soft↗

arXiv2025

Bacteria collective motion is scale-free

Suspensions of swimming bacteria interact hydrodynamically over long ranges, organizing themselves into collective states that drive large-scale chaotic flows, often referred to as "bacterial turbulence". Despite extensive experimental and theoretical work, it remains unclear whether an intrinsic length scale underlies the observed patterns. To shed light on the mechanism driving active turbulence, we investigate the emergence of large-scale flows in E. coli suspensions confined within cylindrical chambers, systematically varying confinement height over more than two orders of magnitude. We first demonstrate that the critical density for the onset of collective motion scales inversely with this confinement height without saturation, even for the smallest densities observed. Near the onset, both the observed length and time scales increase sharply, with the length scale bounded only by the vertical confinement. Importantly, both scales exhibit clear power-law dependence on the confinement height, demonstrating the absence of an intrinsic length scale in bacterial collective motion. This holds up to scales nearly 10,000 times the size of a single bacterium, as evidenced by transient coherent vortices spanning the full chamber width near the onset. Our experimental results demonstrating that bacterial turbulence is scale-free provide important constraints for theories aiming to capture the dynamics of wet active matter.

cond-mat.soft↗

arXiv2025

Active Saffman-Taylor Viscous Fingering

Adding swimming bacteria to a liquid causes its effective shear viscosity to decrease, eventually reaching a regime of zero viscosity. We examined whether this property leads to viscous finger-like displacement fronts like those observed when a less viscous fluid displaces a more viscous liquid. Our study revealed that this system exhibits more complex dynamic characteristics than the classical Saffman-Taylor instability. We discovered that this instability occurs when the bacterial volume fraction exceeds a critical value, and the imposed shear rate is below critical value, for which the viscosity of the suspension is zero.

cond-mat.soft↗

arXiv2022

Dispersion of motile bacteria in a porous medium

Understanding flow and transport of bacteria in porous media is crucial to technologies such as bioremediation, biomineralization or enhanced oil recovery. While physicochemical bacteria filtration is well-documented, recent studies showed that bacterial motility plays a key role in the transport process. Flow and transport experiments performed in microfluidic chips containing randomly placed obstacles confirmed that the distributions of non-motile particles stays compact, whereas for the motile strains, the distributions are characterized by both significant retention as well as fast downstream motion. For motile bacteria, the detailed microscopic study of individual bacteria trajectories reveals two salient features: (i) the emergence of an active retention process triggered by motility, (ii) enhancement of dispersion due to the exchange between fast flow channels and low flow regions in the vicinity of the solid grains. We propose a physical model based on a continuous time random walk approach. This approach accounts for bacteria dispersion via variable pore-scale flow velocities through a Markov model for equidistant particle speeds. Motility of bacteria is modeled by a two-rate trapping process that accounts for the motion towards and active trapping at the obstacles. This approach captures the forward tails observed for the distribution of bacteria displacements, and quantifies an enhanced hydrodynamic dispersion effect that originates in the interaction between flow at the pore-scale and bacterial motility. The model reproduces the experimental observations, and predicts bacteria dispersion and transport at the macroscale.

cond-mat.soft↗

arXiv2019

3D spatial exploration by E. coli echoes motor temporal variability

Unraveling bacterial strategies for spatial exploration is crucial for understanding the complexity in the organization of life. Bacterial motility determines the spatio-temporal structure of microbial communities, controls infection spreading and the microbiota organization in guts or in soils. Most theoretical approaches for modeling bacterial transport rely on their run-and-tumble motion. For Escherichia coli, the run time distribution was reported to follow a Poisson process with a single characteristic time related to the rotational switching of the flagellar motors. However, direct measurements on flagellar motors show heavy-tailed distributions of rotation times stemming from the intrinsic noise in the chemotactic mechanism. Currently, there is no direct experimental evidence that the stochasticity in the chemotactic machinery affect the macroscopic motility of bacteria. In stark contrast with the accepted vision of run-and-tumble, here we report a large behavioral variability of wild-type \emph{E. coli}, revealed in their three-dimensional trajectories. At short observation times, a large distribution of run times is measured on a population and attributed to the slow fluctuations of a signaling protein triggering the flagellar motor reversal. Over long times, individual bacteria undergo significant changes in motility. We demonstrate that such a large distribution of run times introduces measurement biases in most practical situations. Our results reconcile the notorious conundrum between run time observations and motor switching statistics. We finally propose that statistical modeling of transport properties currently undertaken in the emerging framework of active matter studies, should be reconsidered under the scope of this large variability of motility features.

physics.bio-ph↗

arXiv2019

Magnetotactic bacteria in a droplet self-assemble into a rotary motor

From intracellular protein trafficking to large scale motion of animal groups, the physical concepts driving the self-organization of living systems are still largely unraveled. Selforganization of active entities, leading to novel phases and emergent macroscopic properties, recently shed new lights on these complex dynamical processes. Here we show that, under the application of a constant magnetic field, motile magnetotactic bacteria confined in water-in-oil droplets self-assemble into a rotary motor exerting a torque on the external oil phase. A collective motion in the form of a large-scale vortex, reversable by inverting the field direction, builds-up in the droplet with a vorticity perpendicular to the magnetic field. We study this collective organization at different concentrations, magnetic fields and droplets radii and reveal the formation of two torque-generating areas close to the droplet interface. We characterize quantitatively the mechanical energy extractable from this new biological and self-assembled motor.

cond-mat.soft↗

arXiv2018

Effect of motility on the transport of bacteria populations through a porous medium

The role of activity on the hydrodynamic dispersion of bacteria in a model porous medium is studied by tracking thousands of bacteria in a microfluidic chip containing randomly placed pillars. We first evaluate the spreading dynamics of two populations of motile and non-motile bacteria injected at different flow rates. In both cases, we observe that the mean and the variance of the distances covered by the bacteria vary linearly with time and flow velocity, a result qualitatively consistent with the standard geometric dispersion picture. However, quantitatively, the motiles bacteria display a systematic retardation effect when compared to the non-motile ones. Furthermore, the shape of the traveled distance distribution in the flow direction differs significantly for both the motile and the non-motile strain, hence probing a markedly different exploration process. For the non-motile bacteria, the distribution is Gaussian whereas for the motile ones, the distribution displays a positive skewness and spreads exponentially downstream akin to a Gamma distribution. The detailed microscopic study of the trajectories reveals two salient effects characterizing the exploration process of motile bacteria : (i) The emergence of an "active" retention effect due to an extended exploration of the pore surfaces, (ii) an enhanced spreading at the forefront due to the transport of bacteria along "fast-tracks" where they acquire a velocity larger than the local flow velocity. We finally discuss the practical applications of these effects on the large-scale macroscopic transfer and contamination processes caused by microbes in natural environments.

physics.flu-dyn↗

arXiv2018

Actuated rheology of magnetic micro-swimmers suspensions : emergence of motor and brake states

We study the effect of magnetic field on the rheology of magnetic micro-swimmers suspensions. We use a model of a dilute suspension under simple shear and subjected to a constant magnetic field. Particle shear stress is obtained for both pusher and puller types of micro-swimmers. In the limit of low shear rate, the rheology exhibits a constant shear stress, called actuated stress, which only depends on the swimming activity of the particles. This stress is induced by the magnetic field and can be positive (brake state) or negative (motor state). In the limit of low magnetic fields, a scaling relation of the motor-brake effect is derived as a function of the dimensionless parameters of the model. In this case, the shear stress is an affine function of the shear rate. The possibilities offered by such an active system to control the rheological response of a uid are finally discussed.

physics.bio-ph↗

arXiv2015

An individual-based model for biofilm formation at liquid surfaces

The bacterium {\em Bacilus subtilis} frequently forms biofilms at the interface between the culture medium and the air. We develop a mathematical model that couples a description of bacteria as individual discrete objects to the standard advection-diffusion equations for the environment. The model takes into account two different bacterial phenotypes. In the motile state, bacteria swim and perform a run-and-tumble motion that is biased toward regions of high oxygen concentration (aerotaxis). In the matrix-producer state they excrete extracellular polymers, which allows them to connect to other bacteria and to form a biofilm. Bacteria are also advected by the fluid, and can trigger bioconvection. Numerical simulations of the model reproduce all the stages of biofilm formation observed in laboratory experiments. Finally, we study the influence of various model parameters on the dynamics and morphology of biofilms.

q-bio.CB↗

arXiv2015

Turning bacteria suspensions into a "superfluid"

The rheological response under simple shear of an active suspension of Escherichia coli is determined in a large range of shear rates and concentrations. The effective viscosity and the time scales characterizing the bacterial organization under shear are obtained. In the dilute regime, we bring evidences for a low shear Newtonian plateau characterized by a shear viscosity decreasing with concentration. In the semi-dilute regime, for particularly active bacteria, the suspension display a "super-fluid" like transition where the viscous resistance to shear vanishes, thus showing that macroscopically, the activity of pusher swimmers organized by shear, is able to fully overcome the dissipative effects due to viscous loss.

physics.flu-dyn↗

arXiv2008

DNA adsorption at liquid/solid interfaces

DNA adsorption on solid or liquid surfaces is a topic of broad fundamental and applied interest. Here we study by x-ray reflectivity the adsorption of monodisperse double-stranded DNA molecules a positively-charged surface, obtained through chemical grafting of a homogeneous organicmonomolecular layer of N-(2-aminoethyl) dodecanamide on an oxide-free monocrystalline Si(111) wafer. The adsorbed dsDNA is found to embed into the soft monolayer which is deformed in the process. The surface coverage is very high and this adsorbed layer is expected to display 2D nematic ordering.

cond-mat.soft↗