Near field hydrodynamic interactions are essential to determine many important emergent behaviors observed in active suspensions, but have not been successfully modeled so far. In this work we propose an effective model capable of efficiently capturing the essence of the near field hydrodynamic interactions, validated numerically by a pedagogic model system consisting of an E. coli and a spherical tracer. The proposed model effectively captures all the details of near field hydrodynamics through only a tensorial coefficient of resistance, which is fundamentally different from, and thus cannot be replaced by, an effective interaction of conservative nature. In a critical test case that studies the scattering angle of the bacterium-tracer pair dynamics, calculations based on the proposed model reveals a region in parameter space where the bacterium is trapped by the spherical tracer, a phenomenon that is regularly observed in experiments but cannot be explained by any existing model.
As a paradigmatic model of active fluids, bacterial suspensions show intriguing rheological responses drastically different from their counterpart colloidal suspensions. Although the flow of bulk bacterial suspensions has been extensively studied, the rheology of bacterial suspensions under confinement has not been experimentally explored. Here, using a microfluidic viscometer, we systematically measure the rheology of dilute E. coli suspensions under different degrees of confinement. Our study reveals a strong confinement effect: the viscosity of bacterial suspensions decreases substantially …
Bacteria suspension exhibits a wide range of collective phenomena arising from interactions between individual cells. Here we show Serratia marcescens cells near an air-liquid interface spontaneously aggregate into dynamic clusters through surface-mediated hydrodynamic interactions. These long-lived clusters translate randomly and rotate in the counter-clockwise direction; they continuously evolve, merge with others and split into smaller ones. Measurements indicate that long-ranged hydrodynamic interactions have strong influences on cluster properties. Bacterial clusters change material and f…
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 macroscopic…
We experimentally study density fluctuations and energy spectra of bulk \textit{E. coli} suspensions of different concentrations. Our results verify the predicted scaling law of giant number fluctuations in three-dimensional (3D) wet active fluids. We find that such a scaling behavior persists at small scales even in low concentration suspensions well below the transition concentration to active turbulence. Our experiments also support the prediction on the energy spectra of dilute pusher swimmers and illustrate the spectral properties of the active turbulence of dense bacterial suspensions in…
Swimming bacteria create long-range velocity fields that stir a large volume of fluid and move around passive particles dispersed in the fluid. Recent experiments and simulations have shown that long-time mean-squared displacement of passive particles in a bath of swimming bacteria exhibits diffusive behaviour with the effective diffusion coefficient significantly larger than its thermal counterpart. Comprehensive theoretical prediction of this effective diffusion coefficient and understanding of the enhancement mechanism remain a challenge. Here, we adapt the kinetic theory by Lin et al., J. …
Chiral symmetry breaking is ubiquitous in biological systems, from DNA to bacterial suspensions. A key unresolved problem is how chiral structures may spontaneously emerge from achiral interactions. We study a simple model of bacterial suspensions in three dimensions that effectively incorporates active motion and hydrodynamic interactions. We perform large-scale molecular dynamics simulations (up to $10^6$ particles) and describe stable (or long-lived metastable) collective states that exhibit chiral organization although the interactions are achiral. We elucidate under which conditions these…
Active matter is a new class of material, intrinsically out-of equilibrium with intriguing properties. So far, the recent upsurge of studies has mostly focused on the spontaneous behavior of these systems --in the absence of external constraints or driving--. Yet, many real life systems evolve under constraints, being both submitted to flow and various taxis. In the present work, we demonstrate a new experimental system which opens up the way for quantitative investigations, and discriminating examinations, of the challenging theoretical description of such systems. We explore the behavior of …
To survive in harsh conditions, motile bacteria swim in complex environment and respond to the surrounding flow. Here we develop a PDE model describing how the flagella bending affects macroscopic properties of bacterial suspensions. First, we show how the flagella bending contributes to the decrease of the effective viscosity observed in dilute suspension. Our results do not impose tumbling (random re-orientation) as it was done previously to explain the viscosity reduction. Second, we demonstrate a possibility of bacterium escape from the wall entrapment due to the self-induced buckling of f…
We analyse the time dependent non-linear rheology of a dilute bacterial suspension (e.g. E. coli) for a pair of impulsively started linear flows - simple shear and uniaxial extension. The rheology is governed by the bacterium orientation distribution which satisfies a kinetic equation that includes rotation by the imposed flow, and relaxation to isotropy via rotary diffusion and tumbling. The relevant dimensionless parameters are the Peclet number $Pe\equiv \dotγτ$, which dictates the importance of flow-induced orientation anisotropy, and $τD_r$, which quantifies the relative importance of the…
We report a novel form of convection in suspensions of the bioluminiscent marine bacterium $Photobacterium~phosphoreum$. Suspensions of these bacteria placed in a chamber open to the air create persistent luminiscent plumes most easily visible when observed in the dark. These flows are strikingly similar to the classical bioconvection pattern of aerotactic swimming bacteria, which create an unstable stratification by swimming upwards to an air-water interface, but they are a puzzle since the strain of $P.~phosphoreum$ used does not express flagella and therefore cannot swim. Systematic experim…
We probe non-equilibrium properties of an active bacterial bath through measurements of correlations of passive tracer particles and the response function of a driven, optically trapped tracer. These measurements demonstrate violation of the fluctuation-dissipation theorem and enable us to extract the power spectrum of the active stress fluctuations. In some cases, we observe $1/\sqrtω$ scaling in the noise spectrum which we show can be derived from a theoretical model incorporating coupled stress, orientation, and concentration fluctuations of the bacteria.
We describe a new kind of self-propelling motion of bacteria based on the cooperative action of rotating flagella on the surface of bacteria. Describing the ensemble of rotating flagella in the framework of the hydrodynamics with spin the reciprocal theorem of Stokesian hydrodynamics is generalized accordingly. The velocity of the self-propulsion is expressed in terms of the characteristics of the vector field of flagella orientation and it is shown that unusually high velocities of \textit{Thiovulum majus} bacteria may be explained by the cooperative action of the rotating flagella. The expre…
The viscosity of an active suspension of E-Coli bacteria is determined experimentally in the dilute and semi dilute regime using a Y shaped micro-fluidic channel. From the position of the interface between the pure suspending fluid and the suspension, we identify rheo-thickening and rheo-thinning regimes as well as situations at low shear rate where the viscosity of the bacteria suspension can be lower than the viscosity of the suspending fluid. In addition, bacteria concentration and velocity profiles in the bulk are directly measured in the micro-channel.
Active matter such as swarming bacteria and motile colloids exhibits exotic properties different from conventional equilibrium materials. Among these properties, the enhanced diffusion of tracer particles is generally deemed as a hallmark of active matter. Here, rather than spherical tracers, we investigate the diffusion of isolated ellipsoids in quasi-two-dimensional bacterial bath. Our study reveals a nonlinear enhancement of both translational and rotational diffusions. More importantly, we uncover an anomalous coupling between translation and rotation that is strictly prohibited in the cla…
Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and artificial environments. Here, we experimentally investigate sedimentation of passive particles in water containing various concentrations of the bacterium E. coli. Results show that the presence of living bacteria reduces the velocity of the sedimentation front even in the dilute regime, where the sedimentation velocity is expected to be independent of particle concentration. Bacteria increase the effective diffusion coefficient of the passive particles, which determines the width…
The induced diffusion of tracers in a bacterial suspension is studied theoretically and experimentally at low bacterial concentrations. Considering the swimmer-tracer hydrodynamic interactions at low-Reynolds number and using a kinetic theory approach, it is shown that the induced diffusion coefficient is proportional to the swimmer concentration, their mean velocity and a coefficient $β$, as observed experimentally. The coefficient $β$ scales as the tracer-swimmer cross section times the mean square displacement produced by single scatterings. The displacements depend on the swimmer propulsio…
Mixtures of active and passive particles are predicted to exhibit a variety of nonequilibrium phases. Here we report a dynamic clustering phase in mixtures of colloids and motile bacteria. We show that colloidal clustering results from a balance between bond breaking due to persistent active motion and bond stabilization due to torques that align active particle velocity tangentially to the passive particle surface. Furthermore, dynamic clustering spans a broad regime between diffusivity-based and motility-induced phase separation that subsumes typical bacterial motility parameters.
Colloids coupled to a bath of swimming cells generically display enhanced diffusion. This transport dynamics stems from a subtle interplay between the active and passive particles that still resists our understanding despite decades of intense research. Here, we tackle the root of the problem by providing a quantitative characterisation of the single scattering events between a colloid and a bacterium. Based on our experiments, we build a minimal model that quantitatively predicts the geometry of the scattering trajectories, and enhanced colloidal diffusion at long times. This quantitative con…
Bacterial suspensions--a premier example of active fluids--show an unusual response to shear stresses. Instead of increasing the viscosity of the suspending fluid, the emergent collective motions of swimming bacteria can turn a suspension into a "superfluid" with zero apparent viscosity. Although the existence of active "superfluids" has been demonstrated in bulk rheological measurements, the microscopic origin and dynamics of such an exotic phase have not been experimentally probed. Here, using high-speed confocal rheometry, we study the dynamics of concentrated bacterial suspensions under si…
By developing a molecular dynamics model of bacterial chemotaxis, we present the first investigation of tracer statistics in bacterial suspensions where chemotactic effects are considered. We demonstrate that the non-Gaussian statistics of full-coated tracer arises from the athermal bacterial noise. Moreover, Janus (half-coated) tracer performs a composite random walk combining power-law-tail distributed Lévy flights with Brownian jiggling at low coating concentration, but turns to an enhanced directional transport (EDT) when coating concentration is high. Unlike conventional self-propelled pa…
We study the collective dynamics of elongated swimmers in a very thin fluid layer by devising long, filamentous, non-tumbling bacteria. The strong confinement induces weak nematic alignment upon collision, which, for large enough density of cells, gives rise to global nematic order. This homogeneous but fluctuating phase, observed on the largest experimentally-accessible scale of millimeters, exhibits the properties predicted by standard models for flocking such as the Vicsek-style model of polar particles with nematic alignment: true long-range nematic order and non-trivial giant number fluct…
The rheology of semidilute bacterial suspensions is studied with the tools of kinetic theory, considering binary interactions, going beyond the ideal gas approximation. Two models for the interactions are considered, which encompass both the steric and short range interactions. In these, swimmers can either align polarly regardless of the state previous to the collision or they can align axially, being possible the end up antiparallel if the relative angle between directors is large. In both cases, it is found that an ordered phase develops when increasing the density, where the shear stress o…
Swimming microorganisms rely on effective mixing strategies to achieve efficient nutrient influx. Recent experiments, probing the mixing capability of unicellular biflagellates, revealed that passive tracer particles exhibit anomalous non-Gaussian diffusion when immersed in a dilute suspension of self-motile Chlamydomonas reinhardtii algae. Qualitatively, this observation can be explained by the fact that the algae induce a fluid flow that may occasionally accelerate the colloidal tracers to relatively large velocities. A satisfactory quantitative theory of enhanced mixing in dilute active sus…
Active matter exhibits various forms of non-equilibrium states in the absence of external forcing, including macroscopic steady-state currents. Such states are often too complex to be modelled from first principles and our understanding of their physics relies heavily on minimal models. These have mostly been studied in the case of "dry" active matter, where particle dynamics are dominated by friction with their surroundings. Significantly less is known about systems with long-range hydrodynamic interactions that belong to "wet" active matter. Dilute suspensions of motile bacteria, modelled as…
Particle-tracking microrheology of dilute active (self-propelled) colloidal suspensions is studied by considering the external force required to maintain the steady motion of an immersed constant-velocity colloidal probe. If the probe speed is zero, the suspension microstructure is isotropic but exhibits a boundary accumulation of active bath particles at contact due to their self-propulsion. As the probe moves through the suspension, the microstructure is distorted from the nonequilibrium isotropic state, which allows us to define a microviscosity for the suspension using the Stokes drag law.…
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 …
We point out unconventional mechanical properties of confined active fluids, such as bacterial suspensions, under shear. Using a minimal model of an active liquid crystal with no free parameters, we predict the existence of a window of bacteria concentration for which a suspension of \textit{E.~Coli} effectively behaves, at steady-state, as a negative viscosity fluid and reach quantitative agreement with experimental measurements. Our theoretical analysis further shows that a negative apparent viscosity is due to a non-monotonic local velocity profile, and is associated with a non-monotonic st…
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 …
Active particles such as swimming bacteria or self-propelled colloids are known to spontaneously organize into fascinating large-scale dynamic structures. The emergence of these collective states from the motility pattern of the individual particles, typically a random walk, is yet to be probed in a well-defined synthetic system. Here, we report the experimental realization of intermittent colloidal motion that reproduces the run-and-tumble and Levy trajectories common to many swimming and swarming bacteria. Our strategy enables to tailor the sequence of repeated "runs" (nearly constant-speed …
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…
Prior studies have revealed that nonzero odd viscosity is an essential property for chiral active fluids. Here we report that such an odd viscosity also exists in suspensions of non-active or non-externally-driven but chirally-shaped particles. Computational simulations are carried out for monolayers of dense ratchets in simple shear and planar extensional flows. The contact between two ratchets can be either frictionless or infinitely-frictional, depending on their teeth and sliding directions at the contact point. Our results show that the ratchet suspension has the intermediate shear/extens…
Efficient nutrient mixing is crucial for the survival of bacterial colonies and other living systems. This raises the question of whether the optimization of mixing through the emergence of active turbulent motion in bacterial swarms played a role in the evolution of bacterial shapes. Here, to address this question, we solve the hydrodynamic equation for active nematics coupled with an advection-diffusion equation for the nutrients. The latter models a conserved activity field and mimics the conservation of nutrients in bacterial swarms. At the interface between active and passive nematic phas…
The sedimentation process in a suspension of bacteria is the result of the competition between gravity and the intrinsic motion of the microorganisms. We perform simulations of run-and-tumble "squirmers" that move in a fluid medium, focusing on the dependence of the non-equilibrium steady state on the bacterial swimming properties. We find that for high enough activity, the density profiles are no longer simple exponentials; we recover the numerical results via the introduction of a local effective temperature, suggesting that the breakdown of the Perrin-like exponential form is a collective e…
We develop a rigid multiblob method for numerically solving the mobility problem for suspensions of passive and active rigid particles of complex shape in Stokes flow in unconfined, partially confined, and fully confined geometries. As in a number of existing methods, we discretize rigid bodies using a collection of minimally-resolved spherical blobs constrained to move as a rigid body, to arrive at a potentially large linear system of equations for the unknown Lagrange multipliers and rigid-body motions. Here we develop a block-diagonal preconditioner for this linear system and show that a st…
We have developed a lab work module where we teach undergraduate students how to quantify the dynamics of a suspension of microscopic particles, measuring and analyzing the motion of those particles at the individual level or as a group. Differential Dynamic Microscopy (DDM) is a relatively recent technique that precisely does that and constitutes an alternative method to more classical techniques such as dynamics light scattering (DLS) or video particle tracking (VPT). DDM consists in imaging a particle dispersion with a standard light microscope and a camera. The image analysis requires the …
Bacterial processes ranging from gene expression to motility and biofilm formation are constantly challenged by internal and external noise. While the importance of stochastic fluctuations has been appreciated for chemotaxis, it is currently believed that deterministic long-range fluid dynamical effects govern cell-cell and cell-surface scattering - the elementary events that lead to swarming and collective swimming in active suspensions and to the formation of biofilms. Here, we report the first direct measurements of the bacterial flow field generated by individual swimming Escherichia coli …
Self-propelled colloids constitute an important class of intrinsically non-equilibrium matter. Typically, such a particle moves ballistically at short times, but eventually changes its orientation, and displays random-walk behavior in the long-time limit. Theory predicts that if the velocity of non-interacting swimmers varies spatially in 1D, $v(x)$, then their density $ρ(x)$ satisfies $ρ(x) = ρ(0)v(0)/v(x)$, where $x = 0$ is an arbitrary reference point. Such a dependence of steady-state $ρ(x)$ on the particle dynamics, which was the qualitative basis of recent work demonstrating how to `pain…
The unique properties of suspensions containing both active (self-propelling) and passive matter, arising from the nonequilibrium nature of these systems, have been widely studied (e.g., enhanced diffusion, phase separation, and directed motion). Despite this, our understanding of the specific roles played by the relevant parameters of the constituent particles remains incomplete. For instance, to what extent are the velocity and density of swimmers qualitatively distinguishable when it comes to the resultant properties of the suspension as a whole, and when are they merely two different reali…
Flexible filaments and fibres are essential components of important complex fluids that appear in many biological and industrial settings. Direct simulations of these systems that capture the motion and deformation of many immersed filaments in suspension remain a formidable computational challenge due to the complex, coupled fluid--structure interactions of all filaments, the numerical stiffness associated with filament bending, and the various constraints that must be maintained as the filaments deform. In this paper, we address these challenges by describing filament kinematics using quater…
A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific class of self-motile bacterial suspensions is considered as a modeling scenario. To mimic the rod-like geometry of a bacterium, two dissipative particle dynamics particles are connected by a stiff harmonic spring to form an aggregate dissipative particle dynamics molecule. Bacterial motility is modeled through a constant self-propulsion force applied along the…
