Yanan Liu

Dynamique des filaments flexibles et browniens en écoulement visqueux: La dynamique de filaments flexibles individuels en écoulement visqueux est une étape essentielle pour comprendre et contrôler la rhéologie de nombreux fluides complexes. Cette dynamique sous-tend également une multitude de processus biophysiques allant de la propulsion des micro-organismes aux écoulements intracellulaires. Cette thèse présente des expériences systématiques permettant d’étudier la dynamique de filaments flexibles browniens dans un écoulement visqueux. Nous avons choisi d’utiliser un biopolymère, l’actine, comme système modèle de filaments. Sa longueur typique varie de 1 à 100 μm, il est flexible à ces échelles avec une longueur de persistance de l’ordre de 20μm, à cause de ses petites dimensions, il est soumis aux forces Browniennes avec des fluctuations en flexion, et enfin il peut être marqué en fluorescence. Nous utilisons des dispositifs microfluidiques associés à des systèmes de contrôle d’écoulements, un microscope optique équipé́ avec une platine motorisée pour réaliser des expériences contrôlées permettant de suivre la dynamique des filaments d’actine dans un écoulement de cisaillement pur et dans un écoulement élongationnel. Pour les expériences en cisaillement pur, des simulations reproduisant les conditions expérimentales ont aussi été́ menées en utilisant la théorie des poutres inextensibles d’Euler-Bernoulli et la théorie non locale des corps élancés en présence de fluctuations Browniennes et sont en accord quantitatif avec les résultats expérimentaux. Nous montrons que la dynamique des filaments dans ce système est principalement régie par le nombre élasto-visqueux, nombre sans dimension comparant les forces de trainée visqueuses aux forces de flexion élastiques, les fluctuations thermiques ne jouant qu’un rôle secondaire. Nous présentons une caractérisation complète des différents modes de déformation subies par le filament pendant une rotation ainsi que des transitions entre les différents modes. Dans la géométrie élongationnelle, nous avons choisi un canal hyperbolique optimisé pour permettre de longs temps de résidence sous taux de déformation constant. Nous avons observé́ directement la suppression des fluctuations transverse dans la partie extensionnelle tandis que nous observons, dans la partie compressive la formation de structures hélocoïdales tridimensionnelles après le flambage du filament. Pour finir, ce manuscrit de thèse décrit des développements expérimentaux permettant de fabriquer des suspensions de filaments d’actine relativement monodisperse en taille ainsi que des résultats préliminaires sur des effets rhéofluidifiants. Au bilan, les résultats présentes dans ce manuscrit pose les premières pierres de travaux futurs en direction de l’étude de la dynamique de ces filaments dans des écoulements plus complexes comme des écoulements de Poiseuille ou oscillants. Ils permettent aussi d’envisager des études sur le lien entre déformations de particules et propriétés des suspensions diluées d’objets flexibles et Brownien, lien encore peu étudié du point de vue expérimental.

The intricate wobbling motion of flagellated bacteria, characterized by the periodic precession of the cell body, is a determinant factor in their motility and navigation within complex fluid environments. While well-studied in quiescent fluids, bacterial wobbling under ubiquitous flow conditions remains unexplored. In this work, we investigate the wobbling dynamics of \textit{Escherichia coli} swimming near surfaces under steady shear flow. Our experiments reveal that the wobbling amplitude intensifies with flow strength before reaching a plateau, with this amplification exhibiting a strong dependence on the swimming orientation relative to the flow direction. It turns out that the enhanced wobbling remains governed by the misalignment between the cell body and the flagellar bundle. Furthermore, we observe that the wobbling frequency increases monotonically with flow strength, and that shorter bacteria exhibit more pronounced variations in both amplitude and frequency. By linking the wobbling motion to the intrinsic body-flagella misalignment, we attribute the flow-enhanced precession to a combination of shear- and chirality-induced torques acting on the flexible flagellar hook. This mechanical coupling ultimately suppresses the net migration velocity as the flow rate increases. These findings elucidate the elastohydrodynamic mechanisms by which shear flow modifies bacterial locomotion near surfaces, with implications for microbial transport in physiological and ecological environments.

Biological molecules interact with their active and living surroundings, playing a crucial role in a variety of biofunctional processes. However, experimental studies on the morphological changes and diffusion behavior of real bio-macromolecules under active forces remain challenging. Here, suspensions of swimming bacteria at varying number densities are employed as an active bath, with fluorescently dyed DNA chains serving as model biopolymers. Our results show that DNA chains in bacterial baths undergo significant stretching and exhibit repetitive stretching and coiling dynamics, distinctly different from their behavior in thermal baths. The extent of elongation increases linearly with the bacteria density and the correlation length of the flow disturbed by motile bacteria. Furthermore, DNA chains exhibit short-time super-diffusion and long-time normal diffusion, with an effective diffusion coefficient surpassing that of rigid particles with hydrodynamic radii comparable to DNA macromolecules. The stretching deformation also induces anisotropic diffusion in the DNA body frame, characterized by faster transport along the elongated direction attributed to the chain’s incapability to resist bending forces. These findings provide valuable insights into the behavior of chain-like biopolymers in active environments and enhance our understanding of the coupling between the deformation and diffusion of polymers in active systems.

Flagellar-driven locomotion plays a critical role in the bacterial attachment and colonization of surfaces, contributing to the risks of contamination and infection. Extensive efforts to uncover the underlying principles governing bacterial motility near surfaces have relied on idealized assumptions about surrounding artificial surfaces. However, in the context of living systems, the role of cells from tissues and organs becomes increasingly critical, particularly in bacterial swimming and adhesion, yet it remains poorly understood. Here, we propose using biological surfaces composed of vascular endothelial cells to experimentally investigate bacterial motion and interaction behaviors. Our results reveal that bacterial trapping observed on inorganic surfaces is counteractively manifested with reduced radii of circular motion on cellular surfaces. Additionally, two distinct modes of bacterial adhesion were identified: tight and loose adhesion. Interestingly, the presence of living cells enhances bacterial surface enrichment, and imposed flow intensifies this accumulation via a bias-swimming effect. These results surprisingly indicate that physical effects remain the dominant factor regulating bacterial motility and accumulation at the single-cell-layer level in vitro, bridging the gap between simplified hydrodynamic mechanisms and complex biological surfaces with relevance to biofilm formation and bacterial contamination.

Navigating through soft and highly confined environments is crucial for bacteria moving within living organisms' tissues, yet this topic has been less explored. In our study, we experimentally harnessed the unique biconcave geometry of red blood cells (RBCs) to enable real-time visualization of swimming Escherichia coli interacting with soft RBCs. Our findings show that RBCs adhering to a rigid surface can enclose spaces comparable to the size of bacteria, effectively entrapping them. Remarkably, we found that bacteria can escape from this extremely confined space through three newly defined escape modes: Bundling, Unbundling, and Flipping, each mode relying on the specific states of bacterial flagella. A quantitative analysis uncovers significant differences among these modes in terms of scattering angle, escaping speed, and trapping duration. We used two methods to alter the rigidity and adhesion strength of RBCs, and we studied their effects on the detailed bacterial escape process. Our results contribute to the knowledge of bacterial migration in soft, confined spaces, thereby enhancing our understanding of similar processes in biological tissue environments.

The manipulation of magnons in artificial magnonic crystals (MCs) leads to fascinating nonlinear wave phenomena such as the generation of gap solitons, which has been mostly limited to one-dimensional systems. Here, we propose a model system for the magnetization in two-dimensional MCs subjected to a periodic external magnetic field, describing the dynamics of magnetic gap solitons (MGSs) formed by nonlinear self-trapping. We show the formation, stability, and dynamics for various two-dimensional gap modes, including gap solitons and vortical ones. Their existence regions depend on the anisotropic axis orientation of the ferromagnetic film. The Bloch oscillation and depinning propagation of MGSs under constant spin-current injections are discovered and characterized. We design a scheme of pulse-current injection to achieve the distortionless propagation of MGSs. These findings show that the two-dimensional magnonic crystals can be viewed as a building block for MGS-based storage and transmission, where the propagation and localization are variously controlled and reconfigurable.

The study of particle diffusion, a classical conundrum in scientific inquiry, holds manifold implications for various real-world applications. Particularly within the domain of active flows, where the motion of self-propelled particles instigates fluid movement, extensive research has been dedicated to unraveling the dynamics of passive spherical particles. This scrutiny has unearthed intriguing phenomena, such as superdiffusion at brief temporal scales and conventional diffusion at longer intervals. In contrast to the spherical counterparts, anisotropic particles, which manifest directional variations, are prevalent in nature. Although anisotropic behavior in passive fluids has been subject to exploration, enigmatic aspects persist in comprehending the interplay of anisotropic particles within active flows. This research delves into the intricacies of anisotropic passive particle diffusion, exposing a notable escalation in translational and rotational diffusion coefficients, as well as the superdiffusion index, contingent upon bacterial concentration. Through a detailed examination of particle coordinates, the directional preference of particle diffusion is not solely dependent on the particle length, but rather determined by the ratio of the particle length to the associated length scale of the background flow field. These revelations accentuate the paramount importance of unraveling the nuances of anisotropic particle diffusion within the context of active flows. Such insights not only contribute to the fundamental understanding of particle dynamics, but also have potential implications for a spectrum of applications.

Manipulation of magnons in artificial magnonic crystals (MCs) leads to fascinating nonlinear wave phenomena such as the generation of gap solitons, which has been mostly limited to one-dimensional systems. Here, we propose a model system for the magnetization in two-dimensional MCs subjected to a periodic external magnetic field, describing the dynamics of magnetic gap solitons (MGSs) formed by nonlinear self-trapping. We show the formation, stability, and dynamics for various two-dimensional gap modes, including gap solitons and vortical ones. Their existence regions depend on the anisotropic axis orientation of the ferromagnetic film. The Bloch oscillation and depinning propagation of MGSs under constant spin-current injections are discovered and characterized. We design a scheme of pulse current injection to achieve distortionless propagation of MGSs. These findings show that the 2D magnonic crystals can be viewed as a building block for MGSs-based storage and transmission, where the propagation and localization are variously controlled and reconfigurable.

Biopolymers with microscale length and nanoscale cross-sections subjected to active forces is a common non-equilibrium phenomenon in living creatures. It is therefore crucial to intuitively present and investigate the detailed dynamics of such flexible filaments in an active bath full of living matter. Hence, by introducing fluorescent actin filament into an active suspension of motile bacteria at different number densities in a quasi-two-dimensional chamber, we directly visualize the detailed interaction processes and find that bacteria deform a fluctuating filament by relative motion perpendicular to its principal axis of the filament and straighten a filament by parallel motions. We analyzed the evolution of bending energy in dilute and dense bacterial baths with gradual compact or coiled shapes. We successfully introduce a dimensionless number μ ˜ , named as active elasto-viscous number, which governs the generic deformation of filaments in the bacterial baths by comparing the viscous force generated in the bacterial active baths to the elastic restoring force of filaments. The persistence length measuring the tangential correlation of the flexible filament is found to be proportional to μ ˜ . Finally, an effective temperature of the bacterial bath is given through the relation between constant stiffness and loading forces instead of the popularly used Einstein relation. Our findings provide detailed information and specific scaling of flexible filaments interplay with active forces and in response to living and crowded environments.