arXiv subjects

Enkeleida Lushi

Publications and source records attributed to Enkeleida Lushi.

At least 19 recordsLinked to original sources

arXiv2026

Emergence of beating in a magnetic flagellum consisting of active bots

We investigate the emergence of flagellar beating in chains of magnetic self--propelled particles (MSPPs) built from centimeter--scale vibrating robots (Hexbugs) with embedded neodymium dipoles. When one end of the chain is anchored and self--propulsion is activated, longitudinal stress accumulates along the chain until it overcomes the magnetic bending stiffness, triggering a buckling instability that drives sustained flagellar beating. Using a combination of experiments and numerical simulations, we identify three distinct dynamical regimes straight chain, stable flagellar beating, and fission governed by the competition between active force, chain length, and magnetic bending stiffness. The onset of beating requires a seed misalignment set by the balance between magnetic torques and rotational noise, and we show that the transition corresponds to a supercritical Hopf bifurcation. A kinematic model reproduces the observed orientation dynamics with excellent agreement. The magnetic bending stiffness, which arises directly from dipole--dipole interactions, is fully tunable via dipole strength and chain length, offering independent experimental control over both activity and rigidity. Our results establish a macroscopic platform for studying force-induced buckling and self--oscillations in active filaments, with direct connections to flagellar motion in biological and synthetic microswimmers.

cond-mat.soft↗

arXiv2025

Confined floating active carpets generate coherent vortical flows that enhance transport

Slicks are thin viscous films that can be found at the air--water interface of water bodies such as lakes, rivers and oceans. These micro-layers are enriched in surfactants, organic matter, and microorganisms, and exhibit steep physical and chemical gradients across only tens to hundreds of micrometers. In such geometrically confined environments, the hydrodynamics and transport of nutrients, pollutants, and microorganisms are constrained, yet they collectively sustain key biogenic processes. It remains however largely unexplored how the hydrodynamic flows and transport are affected by the vertical extent of slicks relative to the size of microbial colonies. Here, we study this question by combining analytical and numerical approaches to model a microbial colony as an active carpet: a two-dimensional distribution of micro-swimmers exerting dipolar forces. We show that there exists a ratio between the carpet size and the confinement height that is optimal for the enhancement of particle transport toward the colony edges through advective flows that recirculate in 3D vortex-ring-like patterns with a characteristic length comparable to the confinement height. Our results demonstrate that finite, coherent vortex-ring-like structures can arise solely from the geometrical confinement ratio of slick thickness to microbial colony size. These findings shed light on the interplay between collective activity and out-of-equilibrium transport, and on how microbial communities form, spread, and persist in geometrically constrained environments such as surface slicks.

physics.flu-dyn↗

arXiv2025

Micro-swimmer collective dynamics in Brinkman flows

Suspensions of swimming micro-organisms are known to undergo intricate collective dynamics as a result of hydrodynamic and collision interactions. Micro-swimmers, such as bacteria and micro-algae, naturally live and have evolved in complex habitats that include impurities, obstacles and interfaces. To elucidate their dynamics in a heterogeneous environment, we consider a continuum theory where the the micro-swimmers are embedded in a Brinkman wet porous medium, which models viscous flow with an additional resistance or friction due to the presence of smaller stationary obstacles. The conservation equation for the swimmer configurations includes advection and rotation by the immersing fluid, and is coupled to the viscous Brinkman fluid flow with an active stress due to the swimmers' motion in it. Resistance alters individual swimmer locomotion and the way it disturbs the surrounding fluid, and thus it alters its hydrodynamic interactions with others and and such affects collective dynamics.The entropy analysis and the linear stability analysis of the system of equations both reveal that resistance delays and hinders the onset and development of the collective swimming instabilities, and can completely suppress it if sufficiently large. Simulations of the full nonlinear system confirm these. We contrast the results with previous theoretical studies on micro-swimmers in homogeneous viscous flow, and discuss relevant experimental realizations.

physics.flu-dyn↗

arXiv2025

Micro-swimmer locomotion and hydrodynamics in Brinkman Flows

Micro-swimmer locomotion in heterogeneous media is increasingly relevant in biological physics due to the prevalence of microorganisms in complex environments. A model for such porous media is the Brinkman fluid which accounts for a sparse matrix of stationary obstacles via a linear resistance term in the momentum equation. We investigate two models for the locomotion and the flow field generated by a swimmer in such a medium. First, we analyze a dumbbell swimmer composed of two spring-connected spheres and driven by a flagellar force and derive its exact swimming velocity as a function of the Brinkman medium resistance, showing that the swimmer monotonically slows down as the medium drag monotonically increases. In the limit of no resistance the model reduces to the classical Stokes dipole swimmer, while finite resistance introduces hydrodynamic screening that attenuates long-range interactions. Additionally, we derive an analytical expression for the far-field flow generated by a Brinkmanlet force-dipole, which can be used for propulsive point-dipole swimmer models. Remarkably, this approximation reproduces the dumbbell swimmer's flow field in the far-field regime with high accuracy. These results provide new analytical tools for understanding locomotion in complex fluids and offer foundational insights for future studies on collective behavior in active and passive suspensions within porous or structured environments.

physics.flu-dyn↗

arXiv2025

Chemotactic aggregation dynamics of micro-swimmers in Brinkman flows

We study through analysis and simulations of a continuum model the collective chemotactic dynamics of micro-swimmers immersed in viscous Brinkman flows. The Brinkman viscous flow approximates with a resistance or friction term the presence of inert impurities or stationary obstacles immersed in the fluid, an environment that can be regarded as a wet porous medium. Analysis of the linearized system reveals that resistance primarily affects the development of collective swimming instabilities and barely affects chemotactic instabilities. We present a parameter phase space for the distinct types of dynamics we can expect in the case of auto-chemotactic bacteria-like pusher swimmers for varying medium resistance, chemotactic response strength, and hydrodynamic coupling strength values. Simulations of the full nonlinear system show that resistance impacts the collective dynamics for each of these states because it inhibits the hydrodynamic interactions and the emergence of the collective swimmer. Surprisingly, and not expected from the linear analysis predictions, we find that resistance also hampers the chemotactic aggregation of the swimmers because it impedes their ability to navigate efficiently and collectively towards chemical cues and assemble into clusters. We show simulations of the complex system for parameters sets from each of the phase-space regions and quantify the observed behavior. Lastly, we discuss the experimental values of the parameters and discuss possible future experimental realizations of this system.

cond-mat.soft↗

arXiv2023

Cross-stream migration of a vesicle in vortical flows

We use numerical simulations to systematically investigate the vesicle dynamics in two-dimensional (2D) Taylor-Green vortex flow in the absence of inertial forces. Vesicles are highly deformable membranes encapsulating an incompressible fluid and they serve as numerical and experimental proxies for biological cells such as red blood cells. Vesicle dynamics has been studied in free-space/bounded shear, Poiseuille and Taylor-Couette flows in 2D and 3D. Taylor-Green vortex are characterized with even more complicated properties than those flows such as non-uniform flow line curvature, shear gradient. We study the effects of two parameters on the vesicle dynamics: the ratio of the interior fluid viscosity to that of the exterior one and the ratio of the shear forces on the vesicle to the membrane stiffness (characterized by the capillary number). Vesicle deformability nonlinearly depends on these parameters. Although the study is in 2D, our findings contribute to the wide spectrum of intriguing vesicle dynamics: vesicles migrate inwards and eventually rotate at the vortex center if they are sufficiently deformable. If not so, they migrate away from the vortex center and travel across the periodic arrays of vortices.

physics.bio-ph↗

arXiv2020

Metallic Microswimmers Driven up the Wall by Gravity

As a natural and functional behavior, various microorganisms exhibit gravitaxis by orienting and swimming upwards against gravity. Swimming autophoretic nanomotors described herein, comprising bimetallic nanorods, preferentially orient upwards and swim up along a wall, when tail-heavy (i.e. when the density of one of the metals is larger than the other). Through experiment and theory, two mechanisms were identified that contribute to this gravitactic behavior. First, a buoyancy or gravitational torque acts on these rods to align them upwards. Second, hydrodynamic interactions of the rod with the inclined wall induce a fore-aft drag asymmetry on the rods that reinforces their orientation bias and promotes their upward motion.

cond-mat.soft↗

arXiv2019

Relating microswimmer synthesis to rheotactic tunability

We explore the behavior of micron-scale autophoretic Janus (Au/Pt) rods, having various Au/Pt length ratios, swimming near a wall in an imposed background flow. We find that their ability to robustly orient and move upstream, i.e. to rheotax, depends strongly on the Au/Pt ratio, which is easily tunable in synthesis. Numerical simulations of swimming rods actuated by a surface slip show a similar rheotactic tunability when varying the location of the surface slip versus surface drag. Slip location determines whether swimmers are Pushers (rear-actuated), Pullers (front-actuated), or in between. Our simulations and modeling show that Pullers rheotax most robustly due to their larger tilt angle to the wall, which makes them responsive to flow gradients. Thus, rheotactic response infers the nature of difficult to measure flow-fields of an active particle, establishes its dependence on swimmer type, and shows how Janus rods can be tuned for flow responsiveness. We demonstrate the effectiveness of a simple geometric sieve for rheotactic ability.

cond-mat.soft↗

arXiv2017

Scattering of biflagellate microswimmers from surfaces

We use a three-bead-spring model to investigate the dynamics of bi-flagellate micro-swimmers near a surface. While the primary dynamics and scattering are governed by geometric-dependent direct contact, the fluid flows generated by the swimmer locomotion are important in orienting it toward or away from the surface. Flagellar noise and in particular cell spinning about the main axis help a surface-trapped swimmer escape, whereas the time a swimmer spends at the surface depends on the incident angle. The dynamics results from a nuanced interplay of direct collisions, hydrodynamics, noise and the swimmer geometry. We show that to correctly capture the dynamics of a biflagellate swimmer, minimal models need to resolve the shape asymmetry.

physics.bio-ph↗

arXiv2016

Stability and dynamics of anisotropically-tumbling chemotactic swimmers

Micro-swimmers such as bacteria perform random walks known as run-and-tumbles to move up chemo-attractant gradients and as a result aggregate with others. It is also known that such micro-swimmers can self-organize into macroscopic patterns due to interactions with neighboring cells through the fluidic environment they live in. While the pattern formation resulting from chemotactic and hydrodynamic interactions separately and together have been previously investigated, the effect of the anisotropy in the tumbles of micro-swimmers has been unexplored. Here we show through linear analysis and full nonlinear simulations that the slight anisotropy in the individual swimmer tumbles can alter the collective pattern formation in non-trivial ways. We show that tumbling anisotropy diminishes the magnitude of the chemotactic aggregates but may result in more such aggregation peaks.

physics.bio-ph↗

arXiv2016

Collective dynamics in a binary mixture of hydrodynamically coupled micro-rotors

We study, numerically, the collective dynamics of self-rotating nonaligning particles by considering a monolayer of spheres driven by constant clockwise or counterclockwise torques. We show that hydrodynamic interactions alter the emergence of large-scale dynamical patterns compared to those observed in dry systems. In dilute suspensions, the flow stirred by the rotors induces clustering of opposite-spin rotors, while at higher densities same-spin rotors phase separate. Above a critical rotor density, dynamic hexagonal crystals form. Our findings underscore the importance of inclusion of the many-body, long-range hydrodynamic interactions in predicting the phase behavior of active particles.

cond-mat.soft↗

arXiv2016

Directed collective motion of bacteria under channel confinement

Dense suspensions of swimming bacteria are known to exhibit collective behaviour arising from the interplay of steric and hydrodynamic interactions. Unconfined suspensions exhibit transient, recurring vortices and jets, whereas those confinedin circular domains may exhibit order in the form of a spiral vortex. Here we show that confinement into a long and narrow macroscopic `racetrack' geometry stabilises bacterial motion to form a steady unidirectional circulation. This motion is reproduced in simulations of discrete swimmers that reveal the crucial role that bacteria-driven fluid flows play in the dynamics. In particular, cells close to the channel wall produce strong flows which advect cells in the bulk against their swimming direction. We examine in detail the transition from a disordered state to persistent directed motion as a function of the channel width,and show that the width at the crossover point is comparable to the typical correlation length of swirls seen in the unbounded system. Our results shed light on the mechanisms driving the collective behaviour of bacteria and other active matter systems, and stress the importance of the ubiquitous boundaries found in natural habitats.

physics.bio-ph↗

arXiv2016

Dynamics of inert spheres in active suspensions of micro-rotors

Inert particles suspended in active fluids of self-propelled particles are known to often exhibit enhanced diffusion and novel coherent structures. Here we numerically investigate the dynamical behavior and self-organization in a system consisting of passive and actively rotating spheres. The particles interact through direct collisions and the fluid flows generated as they move. In the absence of passive particles, three states emerge in a binary mixture of spinning spheres depending on particle fraction: a dilute gas-like state where the rotors move chaotically, a phase-separated state where like-rotors move in lanes or vortices, and a jammed state where crystals continuously assemble, melt and move (K. Yeo, E. Lushi, and P. M. Vlahovska, Phys. Rev. Lett. 114, 188301 (2015)). Passive particles added to the rotor suspension modify the system dynamics and pattern formation: while states identified in the pure active suspension still emerge, they occur at different densities and mixture proportions. The dynamical behavior of the inert particles is also non-trivially dependent on the system composition.

cond-mat.soft↗

arXiv2015

Microalgae scatter off solid surfaces by hydrodynamic and contact forces

Interactions between microorganisms and solid boundaries play an important role in biological processes, like egg fertilisation, biofilm formation and soil colonisation, where microswimmers move within a structured environment. Despite recent efforts to understand their origin, it is not clear whether these interactions can be understood as fundamentally of hydrodynamic origin or hinging on the swimmer's direct contact with the obstacle. Using a combination of experiments and simulations, here we study in detail the interaction of the biflagellate green alga \textit{Chlamydomonas reinhardtii}, widely used as a model puller microorganism, with convex obstacles, a geometry ideally suited to highlight the different roles of steric and hydrodynamic effects. Our results reveal that both kinds of forces are crucial for the correct description of the interaction of this class of flagellated microorganisms with boundaries.

physics.bio-ph↗

arXiv2015

Periodic and chaotic orbits of plane-confined micro-rotors in creeping flows

We explore theoretically the complex dynamics and emergent behaviors of spinning spheres immersed in viscous fluid. The particles are coupled to each-other via the fluid in which they are suspended: each particle disturbs the surrounding fluid with a rotlet field and that fluid flow affects the motion of the other particles. We notice the emergence of intricate periodic or chaotic trajectories that depend on the rotors initial position and separation. The point-rotor motions confined to a plane bear similarities the classic 2D point-vortex dynamics. Our analyses highlight the complexity of the interaction between just a few rotors and suggest richer behavior in denser populations. We discuss how the model gives insight into more complex systems and suggest possible extensions for future theoretical studies.

physics.flu-dyn↗

arXiv2014

Fluid Flows Created by Swimming Bacteria Drive Self-Organization in Confined Suspensions

Concentrated suspensions of swimming microorganisms and other forms of active matter are known to display complex, self-organized spatio-temporal patterns on scales large compared to those of the individual motile units. Despite intensive experimental and theoretical study, it has remained unclear the extent to which the hydrodynamic flows generated by swimming cells, rather than purely steric interactions between them, drive the self-organization. Here we utilize the recent discovery of a spiral-vortex state in confined suspensions of \textit{B. subtilis} to study this issue in detail. Those experiments showed that if the radius of confinement in a thin cylindrical chamber is below a critical value the suspension will spontaneously form a steady single-vortex state encircled by a counter-rotating cell boundary layer, with spiral cell orientation within the vortex. Left unclear, however, was the flagellar orientation, and hence the cell swimming direction, within the spiral vortex. Here, using a fast simulation method that captures oriented cell-cell and cell-fluid interactions in a minimal model of discrete-particle systems, we predict the striking, counterintuitive result that in the presence of collectively-generated fluid motion the cells within the spiral vortex actually swim upstream against those flows. This is then confirmed by new experiments reported here, which include measurements of flagella bundle orientation and cell tracking in the self-organized state. These results highlight the complex interplay between cell orientation and hydrodynamic flows in concentrated suspensions of microorganisms.

cond-mat.soft↗

arXiv2013

Accumulation of motile elongated micro-organisms in turbulence

We study the effect of turbulence on marine life by performing numerical simulations of motile microorganisms, modelled as prolate spheroids, in isotropic homogeneous turbulence. We show that the clustering and patchiness observed in laminar flows, linear shear and vortex flows, are significantly reduced in a three-dimensional turbulent flow mainly because of the complex topology; elongated micro-orgamisms show some level of clustering in the case of swimmers without any preferential alignment whereas spherical swimmers remain uniformly distributed. Micro-organisms with one preferential swimming direction (e.g. gyrotaxis) still show significant clustering if spherical in shape, whereas prolate swimmers remain more uniformly distributed. Due to their large sensitivity to the local shear, these elongated swimmers react slower to the action of vorticity and gravity and therefore do not have time to accumulate in a turbulent flow. These results show how purely hydrodynamic effects can alter the ecology of microorganisms that can vary their shape and their preferential orientation.

physics.bio-ph↗

arXiv2013

Auto-chemotactic micro-swimmer suspensions: modeling, analysis and simulations

Microorganisms can preferentially orient and move along gradients of a chemo-attractant (i.e., chemotax) while colonies of many microorganisms can collectively undergo complex dynamics in response to chemo-attractants that they themselves produce. For colonies or groups of micro-swimmers we investigate how an "auto-chemotactic" response that should lead to swimmer aggregation is affected by the non-trivial fluid flows that are generated by collective swimming. For this, we consider chemotaxis models based upon a hydrodynamic theory of motile suspensions that are fully coupled to chemo-attractant production, transport, and diffusion. Linear analysis of isotropically ordered suspensions reveals both an aggregative instability due to chemotaxis that occurs independently of swimmer type, and a hydrodynamic instability when the swimmers are "pushers". Nonlinear simulations show nonetheless that hydrodynamic interactions can significantly modify the chemotactically-driven aggregation dynamics in suspensions of "pushers" or "pullers". Different states of the dynamics resulting from these coupled interactions in the colony are discussed.

physics.bio-ph↗