We run numerical simulations of strongly confined suspensions of model spherical swimmers called "squirmers". Because of the confinement, the Stokeslet dipoles generated by the particles are quickly screened and the far-field flow is dominated by the source dipole for all the different kinds of squirmers. However, we show that the collective behavior of the suspension still depends on the self-propelling mechanism of the swimmers as polar states can only be observed for neutral squirmers. We demonstrate that the near-field hydrodynamic interactions play a crucial role in the alignment of the orientation vectors of spherical particles. Moreover, we point out that the enstrophy and the fluid fluctuations of an active suspension also depend on the nature of the squirmers.
In addition to enabling movement towards environments with favourable living conditions, swimming by microorganisms has also been linked to enhanced mixing and improved nutrient uptake by their populations. Experimental studies have shown that Brownian tracer particles exhibit enhanced diffusion due to the swimmers, while theoretical models have linked this increase in diffusion to the flows generated by the swimming microorganisms, as well as collisions with the swimmers. In this study, we perform detailed simulations based on the force-coupling method and its recent extensions to the swimmin…
We present a hydrodynamic study of a monolayer of squirmer model microswimmers confined to a boundary by strong gravity using the simulation method of multi-particle collision dynamics. The squirmers interact with each other via their self-generated hydrodynamic flow fields and thereby form a variety of fascinating dynamic states when density and squirmer type are varied. Weak pushers, neutral squirmers, and pullers have an upright orientation. With their flow fields they push neighbors away and thereby form a hydrodynamic Wigner fluid at lower densities. Furthermore, states of fluctuating cha…
We present a new development of the force-coupling method (FCM) to address the accurate simulation of a large number of interacting micro-swimmers. Our approach is based on the squirmer model, which we adapt to the FCM framework, resulting in a method that is suitable for simulating semi-dilute squirmer suspensions. Other effects, such as steric interactions, are considered with our model. We test our method by comparing the velocity field around a single squirmer and the pairwise interactions between two squirmers with exact solutions to the Stokes equations and results given by other numeric…
A concentrated, vertical monolayer of identical spherical squirmers, which may be bottom-heavy, and which are subjected to a linear shear flow, is modelled computationally by two different methods: Stokesian dynamics, and a lubrication-theory-based method. Inertia is negligible. The aim is to compute the effective shear viscosity and, where possible, the normal stress differences as functions of the areal fraction of spheres $ϕ$, the squirming parameter $β$ (proportional to the ratio of a squirmer's active stresslet to its swimming speed), the ratio $Sq$ of swimming speed to a typical speed of…
The incessant swimming motion of microbes in dense suspensions can give rise to striking collective motions and coherent structures. However, theoretical investigations of these structures typically utilize either computationally demanding numerical simulations, or simplified continuum models. Here we analytically investigate the collective dynamics of a dense array of steady, spherical squirmers. We first calculate the forces and torques acting on two closely-separated squirmers, through solving the Stokes equations to second-order in the ratio of mean spacing to squirmer radius. This lubrica…
Squirmers that are bottom-heavy experience a torque that aligns them along the vertical so that they swim upwards. In a suspension of many squirmers, they also interact hydrodynamically via flow fields that are initiated by their swimming motion and by gravity. Swimming under the combined action of flow field vorticity and gravitational torque is called gyrotaxis. Using the method of multi-particle collision dynamics, we perform hydrodynamic simulations of a many-squirmer system floating above the bottom surface. Due to gyrotaxis they exhibit pronounced cluster formation with increasing gravit…
The dynamic interactions between pairs of swimming microorganisms underpin the collective behaviour of larger suspensions, but accurately calculating pairwise collisions has typically required the use of numerical simulations in which hydrodynamic interactions are fully resolved. In this paper, we utilise analytical expressions for forces and torques acting on two closely separated spherical squirmers -- accurate to second order in the ratio of cell-cell spacing to squirmer radius -- in order to calculate their scattering dynamics. Attention is limited to squirmers whose orientation vectors li…
We study the collective motion of confined spherical microswimmers such as active colloids which we model by so-called squirmers. To simulate hydrodynamic flow fields including thermal noise, we use the method of multi-particle collision dynamics. We demonstrate that hydrodynamic near fields acting between squirmers as well as squirmers and bounding walls crucially determine their collective motion. In particular, with increasing density we observe a clear phase separation into a gas-like and cluster phase for neutral squirmers whereas strong pushers and pullers more gradually approach the hex…
The squirmer is a simple yet instructive model for microswimmers, which employs an effective slip velocity on the surface of a spherical swimmer to describe its self-propulsion. We solve the hydrodynamic flow problem with the lattice Boltzmann (LB) method, which is well-suited for time-dependent problems involving complex boundary conditions. Incorporating the squirmer into LB is relatively straight-forward, but requires an unexpectedly fine grid resolution to capture the physical flow fields and behaviors accurately. We demonstrate this using four basic hydrodynamic tests: Two for the far-fie…
We have shown [J.\ Fluid Mech.\ {\bf 592}, 447 (2007)] that swapping (reversing) trajectories in confined suspension flows prevent collisions between particles approaching each other in adjacent streamlines. Here we demonstrate that by inducing layering this hydrodynamic mechanism changes the microstructure of suspensions in a confined Couette flow. Layers occur either in the near-wall regions or span the whole channel width, depending on the strength of the swapping-trajectory effect. While our theory focuses on dilute suspensions, we postulate that this new hydrodynamic mechanism controls fo…
A mechanistic theory is developed to describe segregation in confined multicomponent suspensions such as blood. It incorporates the two key phenomena arising in these systems at low Reynolds number: hydrodynamic pair collisions and wall-induced migration. In simple shear flow, several regimes of segregation arise, depending on the value of a "margination parameter" M. Most importantly, there is a critical value of M below which a sharp "drainage transition" occurs: one component is completely depleted from the bulk flow to the vicinity of the walls. Direct simulations also exhibit this transit…
We investigate imbibition of a monodisperse emulsion into a low-aspect ratio microfluidic channel with the height h comparable to the droplet diameter d. For confinement ratio d/h = 1.2, the tightly confined disk-like droplets in the channel move more slowly compared to the average suspension velocity. Behind the meniscus that drives the imbibition, there is a droplet-free region, separated from the suspension region by a sharp concentration front. The suspension exhibits strong droplet density and velocity fluctuations, but on average, the suspension domain remains uniform. For weaker confine…
We study theoretically the velocity cross-correlations of a viscous fluid confined in a slit between two viscoelastic media. We analyze the effect of these correlations on the motions of particles suspended in the fluid. The compliance of the confining boundaries gives rise to a long-ranged pair correlation, decaying only as $1/r$ with the interparticle distance $r$. We show how this long-ranged effect may be used to extract the viscoelastic properties of the confining media without embedding tracer particles in them. We discuss the remarkable robustness of such a potential technique with resp…
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. …
Hydrodynamic interactions between particles confined in a liquid-filled linear channel are known to be screened beyond a distance comparable to the channel width. Using a simple analytical theory and lattice-Boltzmann simulations, we show that the hydrodynamic screening is qualitatively modified when the time-dependent response and finite compressibility of the host liquid are taken into account. Diffusive compression modes in the confined liquid cause the particles to have velocity correlations of unbounded range, whose amplitude decays with time only as $t^{-3/2}$.
Flowing blood displays a phenomenon called margination, in which leukocytes and platelets are preferentially found near blood vessel walls, while erythrocytes are depleted from these regions. Here margination is investigated using direct hydrodynamic simulations of a binary suspension of stiff (s) and floppy (f) capsules, as well as a stochastic model that incorporates the key particle transport mechanisms in suspensions -- wall-induced hydrodynamic migration and shear-induced pair collisions. The stochastic model allows the relative importance of these two mechanisms to be directly evaluated …
Similarly to their biological counterparts, suspensions of chemically-active autophoretic swimmers exhibit nontrivial dynamics involving self-organization processes as a result of inter-particle interactions. Using a kinetic model for a dilute suspension of autochemotactic Janus particles, we analyse the effect of a confined pressure-driven flow on these collective behaviours and the impact of chemotactic aggregation on the effective viscosity of the active fluid. Four dynamic regimes are identified when increasing the strength of the imposed pressure-driven flow, each associated with a differ…
We consider the tracer diffusion $D_{rr}$ that arises from the run-and-tumble motion of low Reynolds number swimmers, such as bacteria. In unbounded dilute suspensions, where the dipole swimmers move in uncorrelated runs of length $λ$, an exact solution showed that $D_{rr}$ is independent of $λ$. Here we verify this result in numerical simulations for a particular model swimmer, the spherical squirmer. We also note that in confined microenvironments, such as microscopic droplets, microfluidic devices and bacterial microzones in marine ecosystems, the size of the system can be comparable to $λ$…
Strongly confined active liquids are subject to unique hydrodynamic interactions due to momentum screening and lubricated friction by the confining walls. Using numerical simulations, we demonstrate that 2D dilute suspensions of fore-aft asymmetric polar swimmers in a Hele-Shaw geometry can exhibit a rich variety of novel phase behaviors depending on particle shape, including: coherent polarized density waves with global alignment, stationary asters, persistent counter-rotating vortices, density shocks and rarefaction waves. We also explain these phenomena using a linear stability analysis and…
Intricate fluid displacement patterns, arising from the unstable growth of interfacial perturbations, can be driven by fluid viscoelasticity and surface tension. A soft glassy suspension ages, $i.e.$ its mechanical moduli evolve with time, due to the spontaneous formation of suspension microstructures. The shear and time-dependent rheology of an aging suspension can be exploited to generate a wide variety of interfacial patterns during its displacement by a Newtonian fluid. Using video imaging, we report a rich array of interfacial pattern morphologies: dense viscous, dendritic, viscoelastic f…
Micro-swimmers can serve as cargo carriers that move deep inside complex flow networks. When a school collectively entrains the surrounding fluid, their transport capacity can be enhanced. This effect is quantified with good agreement between experiments with self-propelled droplets and a confined Brinkman squirmer model. The volume of liquid entrained can be much larger than the droplet itself, amplifying the effective cargo capacity over an order of magnitude, even for dilute schools. Hence, biological and engineered swimmers can efficiently transport materials into confined environments.
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 …
Low Reynolds number direct simulations of large populations of hydrodynamically interacting swimming particles confined between planar walls are performed. The results of simulations are compared with a theory that describes dilute suspensions of swimmers. The theory yields scalings with concentration for diffusivities and velocity fluctuations as well as a prediction of the fluid velocity spatial autocorrelation function. Even for uncorrelated swimmers, the theory predicts anticorrelations between nearby fluid elements that correspond to vortex-like swirling motions in the fluid with length s…
Clogging can occur whenever a suspension of particles flows through a confined system. The formation of clogs is often correlated to a reduction in the cross-section of the channel. In this study, we consider the clogging by bridging, i.e., through the formation of a stable arch of particles at a constriction that hinders the transport of particles downstream of the clog. To characterize the role of the volume fraction of the suspension on the clogging dynamics, we study the flow of particulate suspensions through 3D-printed millifluidic devices. We systematically characterize the bridging of …
Phoretic particles self-propel using self-generated physico-chemical gradients at their surface. Within a suspension, they interact hydrodynamically by setting the fluid around them into motion, and chemically by modifying the chemical background seen by their neighbours. While most phoretic systems evolve in confined environments due to buoyancy effects, most models focus on their interactions in unbounded flows. Here, we propose a first model for the interaction of phoretic particles in Hele-Shaw confinement and show that in this limit, hydrodynamic and phoretic interactions share not only t…
We derive a minimal continuum model to investigate the hydrodynamic mechanism behind the fingering instability recently discovered in a suspension of microrollers near a floor [Driscoll et al. Nature Physics, 2016]. Our model, consisting of two continuous lines of rotlets, exhibits a linear instability driven only by hydrodynamics interactions, and reproduces the lengthscale selection observed in large scale particle simulations and in experiments. By adjusting only one parameter, the distance between the two lines, our dispersion relation exhibits quantitative agreement with the simulations a…
We theoretically describe the dynamics of swimmer populations confined in thin liquid films. We first demonstrate that hydrodynamic interactions between confined swimmers only depend on their shape and are independent of their specific swimming mechanism. We also show that due to friction with the walls, confined swimmers do not reorient due to flow gradients but the flow field itself. We then quantify the consequences of these microscopic interaction rules on the large-scale hydrodynamics of isotropic populations. We investigate in details their stability and the resulting phase behavior, hig…
We investigate theoretically and experimentally how the hydrodynamically correlated lateral motion of particles in a suspension confined between two surfaces is affected by the suspension concentration. Despite the long range of the correlations (decaying as 1/r^2 with the inter-particle distance r), the concentration effect is present only at short inter-particle distances for which the static pair correlation is nonuniform. This is in sharp contrast with the effect of hydrodynamic screening present in unconfined suspensions, where increasing the concentration changes the prefactor of the lar…
Hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls are studied under creeping-flow conditions. The many-particle friction matrix in this system is evaluated using our novel numerical algorithm based on transformations between Cartesian and spherical representations of Stokes flow. The Cartesian representation is used to describe the interaction of the fluid with the walls and the spherical representation is used to describe the interaction with the particles. The transformations between these two representations are given in a closed for…
We analyze a dilute suspension of active particles confined between walls and subjected to fields that can modulate particle speed as well as orientation. Generally, the particle distribution is different in the bulk compared to near the walls. In the bulk, particles tend to accumulate in the regions of low speed, but in the presence of an orienting field, particles rotate to align with the field and accumulate downstream in the field direction. At the walls, particles tend to accumulate pointing into the walls and thereby exert pressure on walls. But the presence of strong orienting fields ca…
We present experimental observations of the spatial distribution of large inertial particles suspended in a turbulent swirling flow at high Reynolds number. The plastic particles, which are tracked using several high speed cameras, are heavier than the working fluid so that their dynamics results from a competition between gravitational effects and turbulent agitation. We observe two different regimes of suspension. At low rotation rate, particles are strongly confined close to the bottom and are not able to reach the upper region of the tank whatever their size or density. At high rotation ra…
We investigate the rheology of strain-hardening spherical capsules, from the dilute to the concentrated regime under a confined shear flow using three-dimensional numerical simulations. We consider the effect of capillary number, volume fraction and membrane inextensibility on the particle deformation and on the effective suspension viscosity and normal stress differences of the suspension. The suspension displays a shear-thinning behaviour which is a characteristic of soft particles such as emulsion droplets, vesicles, strain-softening capsules, and red blood cells. We find that the membrane …
We have studied experimentally particle suspension when injecting a gas at the bottom of an immersed granular layer confined in a Hele-Shaw cell. This work focuses on the dynamics of particles slightly denser than the surrounding fluid. The gas, injected at constant flow-rate, rises through the granular bed then forms bubbles which entrain particles in the above liquid layer. The particles settle down on the edges of the cell, avalanche on the crater formed at the granular bed free surface, and are further entrained by the continuous bubbling at the center. We report the existence of a station…
The structure and dynamics of confined suspensions of particles of arbitrary shape is of interest in multiple disciplines, from biology to engineering. Theoretical studies are often limited by the complexity of long-range particle-particle and particle-wall forces, including many-body fluctuating hydrodynamic interactions. Here, we report a computational study on the diffusion of spherical and cylindrical particles confined in a spherical cavity. We rely on an Immersed-Boundary General geometry Ewald-like method to capture lubrication and long-range hydrodynamics, and include appropriate non-s…
Recent experimental studies have shown that confinement can profoundly affect self-organization in semi-dilute active suspensions, leading to striking features such as the formation of steady and spontaneous vortices in circular domains and the emergence of unidirectional pumping motions in periodic racetrack geometries. Motivated by these findings, we analyze the two-dimensional dynamics in confined suspensions of active self-propelled swimmers using a mean-field kinetic theory where conservation equations for the particle configurations are coupled to the forced Navier-Stokes equations for t…
Driven or active suspensions can display fascinating collective behavior, where coherent motions or structures arise on a scale much larger than that of the constituent particles. Here, we report experiments and numerical simulations revealing that red blood cells (RBCs) assemble into regular patterns in a confined shear flow. The order is of pure hydrodynamic and inertialess origin, and emerges from a subtle interplay between (i) hydrodynamic repulsion by the bounding walls which drives deformable cells towards the channel mid-plane and (ii) intercellular hydrodynamic interactions which can b…
We study a collection of polar self-propelled particles confined to a long two-dimensional channel. We write the coupled hydrodynamic equations of motion for density and polarisation order parameter. At two confined boundaries, density is fixed to the mean and orientation is anti-parallel with fixed magnitude of polarisation. Such boundary conditions make our system similar to a sheared suspension of self-propelled particles, which has many practical applications. Antiparallel alignment at the two confined boundaries and alignment inside the channel create rolls of orientation along the long a…
