arXiv subjects

Gaspard Junot

Publications and source records attributed to Gaspard Junot.

10 recordsLinked to original sources

arXiv2025

Confinement controls bacterial spreading at all scales

Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species alternate between bulk and surface motion displaying in each case, distinct kinematics. This inherent complexity is key to many practical biological and ecological issues involving spreading and contamination, essential for understanding the spatiotemporal structuring of populations in their environment. However grasping the interplay between geometrical confinement and kinematics driven by internal biological responses remains poorly understood from a physical and biological standpoint. Here, we address this question through experimental and theoretical analysis in the heuristic situation of two parallel confining surfaces. We track wild-type E. coli - a model peritrichous flagellated bacterium - in 3D over extended periods of time. We obtain the first experimental measurements of the emerging diffusivity and bulk/surface residence times as a function of confinement height and the specific chiral kinematics at surfaces. All experimental results are quantitatively reproduced, without parametric adjustment, by a non-Markovian stochastic (BV) model that incorporates the internal biochemical memory carried by a phosphorylated protein switching the motor rotation. By matching the results with a Markovian (memoryless) companion model, we derive an analytical expression for the diffusivity and demonstrate how confining walls influence microbial long-range dispersion. This approach also provides a general conceptual basis for understanding how microorganisms navigate complex environments, in which their movement alternates between bulk and surfaces.

physics.bio-ph↗

arXiv2024

Molecular Dynamics Simulations of Microscopic Structural Transition and Macroscopic Mechanical Properties of Magnetic Gels

Magnetic gels with embedded micro/nano-sized magnetic particles in crosslinked polymer networks can be actuated by external magnetic fields, with changes in their internal microscopic structures and macroscopic mechanical properties. We investigate the responses of such magnetic gels to an external magnetic field, by means of coarse-grained molecular dynamics simulations. We find that the dynamics of magnetic particles are determined by the interplay of between magnetic dipole-dipole interactions, polymer elasticity and thermal fluctuations. The corresponding microscopic structures formed by the magnetic particles such as elongated chains can be controlled by the external magnetic field. Furthermore, the magnetic gels can exhibit reinforced macroscopic mechanical properties, where the elastic modulus increases algebraically with the magnetic moments of the particles in the form of $\propto(m-m_{\mathrm{c}})^{2}$ when magnetic chains are formed. This simulation work can not only serve as a tool for studying the microscopic and the macroscopic responses of the magnetic gels, but also facilitate future fabrications and practical controls of magnetic composites with desired physical properties.

cond-mat.soft↗

arXiv2024

Bidirectional Zigzag Growth from Clusters of Active Colloidal Shakers

Driven or self-propelling particles moving in viscoelastic fluids recently emerge as novel class of active systems showing a complex yet rich set of phenomena due to the non-Newtonian nature of the dispersing medium. Here we investigate the one-dimensional growth of clusters made of active colloidal shakers, which are realized by oscillating magnetic rotors dispersed within a viscoelastic fluid and at different concentration of the dissolved polymer. These magnetic particles when actuated by an oscillating field display a flow profile similar to that of a shaker force dipole, i.e. without any net propulsion. We design a protocol to assemble clusters of colloidal shakers and induce their controlled expansion into elongated zigzag structures. We observe a power law growth of the mean chain length and use theoretical arguments to explain the measured $1/3$ exponent. These arguments agree well with both experiments and particle based numerical simulations.

cond-mat.soft↗

arXiv2024

Large scale zigzag pattern emerging from circulating active shakers

We report the emergence of large zigzag bands in a population of reversibly actuated magnetic rotors that behave as active shakers, namely squirmers that shake the fluid around them without moving. The shakers collectively organize into dynamic structures displaying self-similar growth, and generate topological defects in form of cusps that connect vortices of rolling particles with alternating chirality. By combining experimental analysis with particle-based simulation, we show that the special flow field created by the shakers is the only ingredient needed to reproduce the observed spatiotemporal pattern. We unveil a self-organization scenario in a collection of driven particles in an viscoelastic medium emerging from the reduced particle degrees of freedom, as here the frozen orientational motion of the shakers.

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↗

arXiv2021

Collective hydrodynamic transport of magnetic microrollers

We investigate the collective transport properties of microscopic magnetic rollers that propel close to a surface due to a circularly polarized, rotating magnetic field. The applied field exerts a torque to the particles, which induces a net rolling motion close to a surface. The collective dynamics of the particles result from the balance between magnetic dipolar interactions and hydrodynamic ones. We show that, when hydrodynamics dominate, i.e. for high particle spinning, the collective mean velocity linearly increases with the particle density. In this regime we analyse the clustering kinetics, and find that hydrodynamic interactions between the anisotropic, elongated particles, induce preferential cluster growth along a direction perpendicular to the driving one, leading to dynamic clusters that easily break and reform during propulsion.

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↗

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

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

Oscillatory surface rheotaxis of swimming E. coli bacteria

Bacterial contamination of biological conducts, catheters or water resources is a major threat to public health and can be amplified by the ability of bacteria to swim upstream. The mechanisms of this rheotaxis, the reorientation with respect to flow gradients, often in complex and confined environments, are still poorly understood. Here, we follow individual E. coli bacteria swimming at surfaces under shear flow with two complementary experimental assays, based on 3D Lagrangian tracking and fluorescent flagellar labelling and we develop a theoretical model for their rheotactic motion. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A full theoretical analysis explains these regimes and predicts the corresponding critical shear rates. The predicted transitions as well as the oscillation dynamics are in good agreement with experimental observations. Our results shed new light on bacterial transport and reveal new strategies for contamination prevention.

cond-mat.soft↗