arXiv subjects

Harold Auradou

Publications and source records attributed to Harold Auradou.

At least 19 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↗

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↗

arXiv2023

Ostwald-like ripening in the two-dimensional clustering of passive particles induced by swimming bacteria

Clustering passive particles by active agents is a promising route for fabrication of colloidal structures. Here, we report the dynamic clustering of micrometric beads in a suspension of motile bacteria. We characterize the coarsening dynamics for various bead sizes, surface fractions and bacterial concentrations. We show that the time scale $τ$ for the onset of clustering is governed by the time of first encounter of diffusing beads. At large time ($t \gg τ$), we observe a robust cluster growth as $t^{1/3}$, similar to the Ostwald ripening mechanism. From bead tracking measurements, we extract the short-range bacteria-induced attractive force at the origin of this clustering.

cond-mat.soft↗

arXiv2022

Run-to-Tumble Variability Controls the Surface Residence Times of ${\it E.~coli}$ Bacteria

Motile bacteria are known to accumulate at surfaces, eventually leading to changes in bacterial motility and bio-film formation. We use a novel two-colour, three-dimensional Lagrangian tracking technique, to follow simultaneously the body and the flagella of a wild-type ${\it Escherichia~coli}$. We observe long surface residence times and surface escape corresponding mostly to immediately antecedent tumbling. A motility model accounting for a large behavioural variability in run-time duration, reproduces all experimental findings and gives new insights into surface trapping efficiency.

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↗

arXiv2021

Single-Trajectory Characterization of Active Swimmers in a Flow

We develop a maximum likelihood method to infer relevant physical properties of elongated active particles. Using individual trajectories of advected swimmers as input, we are able to accurately determine their rotational diffusion coefficients and an effective measure of their aspect ratio, also providing reliable estimators for the uncertainties of such quantities. We validate our theoretical construction using numerically generated active trajectories upon no-flow, simple shear, and Poiseuille flow, with excellent results. Being designed to rely on single-particle data, our method eases applications in experimental conditions where swimmers exhibit a strong morphological diversity. We briefly discuss some of such ongoing experimental applications, specifically, in the characterization of swimming E.coli in a flow.

cond-mat.soft↗

arXiv2020

The Influence of Motility on Bacterial Accumulation in a Microporous Channel

We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid body which is propelled by a force-free mechanism. To account for the behavior of living bacteria, the model also incorporates a run-and-tumble process. The model bacteria are capable of hydrodynamically interacting with both of the channel walls and the obstacle. This enables the bacteria to get reoriented when experiencing a shear-flow. We demonstrate that this model is capable of reproducing the bacterial accumulation on the rear side of an obstacle, as has recently been experimentally observed by [G. L. Mino, et al., Advances in Microbiology 8, 451 (2018)] using E.coli bacteria. By systematically varying the external flow strength and the motility of the bacteria, we resolve the interplay between the local flow strength and the swimming characteristics that lead to the accumulation. Moreover, by changing the geometry of the channel, we also reveal the important role of the interactions between the bacteria and the confining walls for the accumulation process.

cond-mat.soft↗

arXiv2019

Swimming bacteria in Poiseuille flow: the quest for active Bretherton-Jeffery trajectories

Using a 3D Lagrangian tracking technique, we determine experimentally the trajectories of non-tumbling E. coli mutants swimming in a Poiseuille flow. We identify a typology of trajectories in agreement with a kinematic "active Bretherton-Jeffery" model, featuring an axi-symmetric self-propelled ellipsoid. In particular, we recover the "swinging" and "shear tumbling" kinematics predicted theoretically by Zöttl et al. Moreover using this model, we derive analytically new features such as quasi-planar piece-wise trajectories, associated with the high aspect ratio of the bacteria, as well as the existence of a drift angle around which bacteria perform closed cyclic trajectories. However, the agreement between the model predictions and the experimental results remains local in time, due to the presence of Brownian rotational noise.

physics.flu-dyn↗

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↗

arXiv2016

Large scale flow visualization and anemometry applied to lab on chip models of porous media

The following is a report on an experimental technique allowing to quantify and map the velocity field with a very high resolution and a simple equipment in large 2D devices. A simple Shlieren technique is proposed to reinforce the contrast in the images and allow you to detect seeded particles that are pixel-sized or even inferior to it. The velocimetry technique that we have reported on is based on auto-correlation functions of the pixel intensity, which we have shown are directly related to the magnitude of the local average velocity. The characteristic time involved in the decorrelation of the signal is proportional to the tracer size and inversely proportional to the average velocity. We have reported on a detailed discussion about the optimization of relevant involved parameters, the spatial resolution and the accuracy of the method. The technique is then applied to a model porous media made of a random channel network. We show that it is highly efficient to determine the magnitude of the flow in each of the channels of the network, opening the road to the fundamental study of the flows of complex fluids. The latter is illustrated with yield stress fluid, in which the flow becomes highly heterogeneous at small flow rates.

physics.flu-dyn↗

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↗

arXiv2015

Effect of the porosity on the fracture surface roughness of sintered materials: From anisotropic to isotropic self-affine scaling

To unravel how the microstructure affects the fracture surface roughness in heterogeneous brittle solids like rocks or ceramics, we characterized the roughness statistics of post-mortem fracture surfaces in home-made materials of adjustable microstructure length-scale and porosity, obtained by sintering monodisperse polystyrene beads. Beyond the characteristic size of disorder, the roughness profiles are found to exhibit self-affine scaling features evolving with porosity. Starting from a null value and increasing the porosity, we quantitatively modify the self-affine scaling properties from anisotropic (at low porosity) to isotropic (for porosity larger than 10 %).

cond-mat.mtrl-sci↗

arXiv2013

Transverse and lateral confinement effects on the oscillations of a free cylinder in a viscous flow

The different types of instabilities of free cylinders (diameter $D$, length $L$) have been studied in a viscous flow (velocity $U$) between parallel vertical walls of horizontal width $W$ at a distance $H$: the influence of the confinement parameters $D/H$ and $L/W$ has been investigated. As $D/H$ increases, there is a transition from stable flow to oscillations transverse to the walls and then to a fluttering motion with oscillations of the angle of the axis with respect to the horizontal. The two types of oscillations may be superimposed in the transition domain. The frequency $f$ of the transverse oscillations is independent of the lateral confinement $L/W$ in the range: 0.055 \le L/W \le 0.94$ for a given cylinder velocity $V_{cx}$ and increases only weakly with $V_{cx}$. These results are accounted for by assuming a 2D local flow over the cylinder with a characteristic velocity independent of $L/W$ for a given $V_{cx}$ value. The experimental values of $f$ are also independent of the transverse confinement $D/H$. The frequency $f_f$ of the fluttering motion is significantly lower than $f$: $f_f$ is also nearly independent of the cylinder diameter and of the flow velocity but decreases significantly as $L/W$ increases. The fluttering instability is then rather a 3D phenomenon involving the full length of the cylinder and the clearance between its ends and the side walls.

physics.flu-dyn↗

arXiv2012

Self-Sustained Reaction Fronts in Porous Media

We analyze experimentally chemical waves propagation in the disordered flow field of a porous medium. The reaction fronts travel at a constant velocity which drastically depends on the mean flow direction and rate. The fronts may propagate either downstream and upstream but, surprisingly, they remain static over a range of flow rate values. Resulting from the competition between the chemical reaction and the disordered flow field, these frozen fronts display a particular sawtooth shape. The frozen regime is likely to be associated with front pinning in low velocity zones, the number of which varies with the ratio of the mean flow and the chemical front velocities.

cond-mat.dis-nn↗

arXiv2012

Relation Between First Arrival Time and Permeability in Self-Affine Fractures with Areas in Contact

We demonstrate that the first arrival time in dispersive processes in self-affine fractures are governed by the same length scale characterizing the fractures as that which controls their permeability. In one-dimensional channel flow this length scale is the aperture of the bottle neck, i.e., the region having the smallest aperture. In two dimensions, the concept of a bottle neck is generalized to that of a minimal path normal to the flow. The length scale is then the average aperture along this path. There is a linear relationship between the first arrival time and this length scale, even when there is strong overlap between the fracture surfaces creating areas with zero permeability. We express the first arrival time directly in terms of the permeability.

physics.flu-dyn↗

arXiv2012

Stokes flow paths separation and recirculation cells in X-junctions of varying angle

Fluid and solute transfer in X-junctions between straight channels is shown to depend critically on the junction angle in the Stokes flow regime. Experimentally, water and a water-dye solution are injected at equal flow rates in two facing channels of the junction: Planar Laser Induced fluorescence (PLIF) measurements show that the largest part of each injected fluid "bounces back" preferentially into the outlet channel at the lowest angle to the injection; this is opposite to the inertial case and requires a high curvature of the corresponding streamlines. The proportion of this fluid in the other channel decreases from 50% at 90\degree to zero at a threshold angle. These counterintuitive features reflect the minimization of energy dissipation for Stokes flows. Finite elements numerical simulations of a 2D Stokes flow of equivalent geometry con rm these results and show that, below the threshold angle 33.8\degree recirculation cells are present in the center part of the junction and separate the two injected flows of the two solutions. Reducing further leads to the appearance of new recirculation cells with lower flow velocities.

physics.flu-dyn↗

arXiv2012

Oscillations and translation of a free cylinder in a confined flow

An oscillatory instability has been observed experimentally on an horizontal cylinder free to move and rotate between two parallel vertical walls of distance H; its characteristics differ both from vortex shedding driven oscillations and from those of tethered cylinders in the same geometry. The vertical motion of the cylinder, its rotation about its axis and its transverse motion across the gap have been investigated as a function of its diameter D, its density s, of the mean vertical velocity U of the fluid and of its viscosity. For a blockage ratio D/H above 0.5 and a Reynolds number Re larger then 14, oscillations of the rolling angle of the cylinder about its axis and of its transverse coordinate in the gap are observed together with periodic variations of the vertical velocity. Their frequency f is the same for the sedimentation of the cylinder in a static fluid (U = 0) and for a non-zero mean flow (U 6= 0). The Strouhal number St associated to the oscillation varies as 1/Re with : St.Re = 3 $\pm$ 0.15. The corresponding period 1/f is then independent of U and corresponds to a characteristic viscous diffusion time over a distance ~ D, implying a strong influence of the viscosity. These characteristics differ from those of vortex shedding and tethered cylinders for which St is instead roughly constant with Re and higher than here.

physics.flu-dyn↗

arXiv2010

Permeability Estimates of Self-Affine Fracture Faults Based on Generalization of the Bottle Neck Concept

We propose a method for calculating the effective permeability of two-dimensional self-affine permeability fields based on generalizing the one-dimensional concept of a bottleneck. We test the method on fracture faults where the local permeability field is given by the cube of the aperture field. The method remains accurate even when there is substantial mechanical overlap between the two fracture surfaces. The computational efficiency of the method is comparable to calculating a simple average and is more than two orders of magnitude faster than solving the Reynolds equations using a finite-difference scheme.

physics.flu-dyn↗