We obtain hydrodynamic equations describing a fluid consisting of chiral molecules or a suspension of chiral particles in a Newtonian fluid. The stresses arising in a flowing chiral liquid have a component forbidden by symmetry in a Newtonian liquid. For example, a chiral liquid in a Poiseuille flow between parallel plates exerts forces on the plates, which are perpendicular to the flow. A generic flow results in spatial separation of particles of different chirality. Thus even a racemic suspension will exhibit chiral properties in a generic flow. A suspension of particles of random shape in a Newtonian liquid is described by equations which are similar to those describing a racemic mixture of chiral particles in a liquid.
We simulate with hydrodynamics a suspension of active disks squirming through a Newtonian fluid. We explore numerically the full range of squirmer area fractions from dilute to close packed and show that "motility induced phase separation" (MIPS), which was recently proposed to arise generically in active matter, and which has been seen in simulations of active Brownian disks, is strongly suppressed by hydrodynamic interactions. We give an argument for why this should be the case and support it with counterpart simulations of active Brownian disks in a parameter regime that provides a closer c…
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…
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…
Using a simple model of self-propelled particle, the effective shear viscosity of a dilute, spatially homogeneous suspension of active particles is studied. We use formulation of non-linear Fokker-Planck equation to drive a kinetic description, including the effect of external flow field, rotary diffusion, and particle-particle hydrodynamic interactions in two dimensions. Analytical expressions are obtained for the stress tensor at small Peclet numbers, in a simple shear flow, up to second order of volume fraction of the swimmers, which shows the explicit dependence of shear viscosity on the d…
The lack of detailed balance in active colloidal suspensions allows dissipation to determine stationary states. Here we show that slow viscous flow produced by polar or apolar active colloids near plane walls mediates attractive hydrodynamic forces that drive crystallization. Hydrodynamically mediated torques tend to destabilize the crystal but stability can be regained through critical amounts of bottom-heaviness or chiral activity. Numerical simulations show that crystallization is not nucleational, as in equilibrium, but is preceded by a spinodal-like instability. Harmonic excitations of th…
A universal characteristic of mesoscale turbulence in active suspensions is the emergence of a typical vortex length scale, distinctly different from the scale-invariance of turbulent high-Reynolds number flows. Collective length-scale selection has been observed in bacterial fluids, endothelial tissue and active colloides, yet the physical origins of this phenomenon remain elusive. Here, we systematically derive an effective fourth-order field theory from a generic microscopic model that allows us to predict the typical vortex size in microswimmer suspensions. Building on a self-consistent cl…
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…
Understanding the correlation between structure and rheology in colloidal suspensions is important as these suspensions are crucial in industrial applications. Moreover, colloids exhibit a wide range of structures under confinement that could considerably alter the viscosity. Here, we use a combination of experiments and simulations to elucidate how confinement induced structures alter the relative contributions of hydrodynamic and repulsive forces to produce up to a ten fold change in the viscosity. We use a custom built confocal rheoscope to image the particle configurations of a colloidal s…
Active fluids comprise a variety of systems composed of elements immersed in a fluid environment which can convert some form of energy into directed motion; as such they are intrinsically out-of-equilibrium in the absence of any external forcing. A fundamental problem in the physics of active matter concerns the understanding of how the characteristics of the autonomous propulsion and agent-agent interactions determine the collective dynamics of the system. We study numerically suspensions of self-propelled diffusiophoretic colloids, in (quasi)-2d configurations, accounting for both dynamicall…
We study the role of hydrodynamic interactions in the collective behaviour of collections of microscopic active particles suspended in a fluid. We introduce a novel calculational framework that allows us to separate the different contributions to their collective dynamics from hydrodynamic interactions on different length scales. Hence we are able to systematically show that lubrication forces when the particles are very close to each other play as important a role as long-range hydrodynamic interactions in determining their many-body behaviour. We find that motility-induced phase separation i…
The rotational Brownian motion of colloidal spheres in dense suspensions reflects local hydrodynamics and friction, both key to non-linear rheological phenomena such as shear-thickening and jamming, and transport in crowded environments, including intracellular migration and blood flow. To fully elucidate the role of rotational dynamics experimentally, it is crucial to measure the translational and rotational motion of all spheres simultaneously. Here, we develop compositionally uniform colloidal spheres with an off-centre, fully embedded core with a different fluorophore to the particle body,…
For suspensions of permeable particles, the short-time translational and rotational self-diffusion coefficients, and collective diffusion and sedimentation coefficients are evaluated theoretically. An individual particle is modeled as a uniformly permeable sphere of a given permeability, with the internal solvent flow described by the Debye-Bueche-Brinkman equation. The particles are assumed to interact non-hydrodynamically by their excluded volumes. The virial expansion of the transport properties in powers of the volume fraction is performed up to the two-particle level. The first-order viri…
We propose a method to parameterize a coarse grained model for the hydrodynamic friction between nearly touching rough spheres in suspension flows. The frictional resistance due to surface roughness primarily alters the sliding and rolling modes of motion of rough particles. Stokesian dynamics simulations incorporating a near-field pairwise resistance model accounting for these enhanced frictional modes were employed to compute particle trajectories in shear flow. In this model, the resistance to sliding and rolling modes of motion are augmented from a weakly diverging log$(1/h)$ form for smoo…
Diffusion in bidisperse Brownian hard-sphere suspensions is studied by Stokesian Dynamics (SD) computer simulations and a semi-analytical theoretical scheme for colloidal short-time dynamics, based on Beenakker and Mazur's method [Physica 120A, 388 (1983) & 126A, 349 (1984)]. Two species of hard spheres are suspended in an overdamped viscous solvent that mediates the salient hydrodynamic interactions among all particles. In a comprehensive parameter scan that covers various packing fractions and suspension compositions, we employ numerically accurate SD simulations to compute the initial diffu…
We present a computer simulation study on the crystal nucleation process in suspensions of hard spheres, fully taking into account the solvent hydrodynamics. If the dynamics of collodial crystallization were purely diffusive, the crystal nucleation rate densities would drop as the inverse of the solvent viscosity. However, we observe that the nucleation rate densities do not scale in this way, but are enhanced at high viscosities. This effect might explain the large discrepancy between the nuclation rate densities obtained by simulation and experiment that have reported in the literature so fa…
We present an easy-to-use analytic toolbox for the calculation of short-time transport properties of concentrated suspensions of spherical colloidal particles with internal hydrodynamic structure, and direct interactions described by a hard-core or soft Hertz pair potential. The considered dynamic properties include self-diffusion and sedimentation coefficients, the wavenumber-dependent diffusion function determined in dynamic scattering experiments, and the high-frequency shear viscosity. The toolbox is based on the hydrodynamic radius model (HRM) wherein the internal particle structure is ma…
We combine experiments, large scale simulations and continuum models to study the emergence of coherent structures in a suspension of magnetically driven microrollers sedimented near a floor. Collective hydrodynamic effects are predominant in this system, leading to strong density-velocity coupling. We characterize a uniform suspension and show that density waves propagate freely in all directions in a dispersive fashion. When sharp density gradients are introduced in the suspension, we observe the formation of a shock. Unlike Burgers' shock-like structures observed in other active and driven …
Ordered phases emerged in active suspensions of polar swimmers are under long-wavelength hydrodynamic mediated instabilities. In this letter, we show that chemical molecules dissolved in aqueous suspensions, as an unavoidable part of most wet active systems, can mediate long-range interactions and subsequently stabilize the ordered phases. Chemoattractant in living suspensions and dissolved molecules producing phoretic forces in synthesized Janus suspensions are reminiscent of such molecules. Communication between swimmers through the gradients of such chemicals generated by individual swimmer…
Evolution of a suspension drop entrained by Poiseuille flow is studied numerically at a low Reynolds number. A suspension drop is modelled by a cloud of many non-touching particles, initially randomly distributed inside a spherical volume of a viscous fluid which is identical to the host fluid outside the drop. Evolution of particle positions and velocities is evaluated by the accurate multipole method corrected for lubrication, implemented in the {\sc hydromultipole} numerical code. Deformation of the drop is shown to be smaller for a larger volume fraction. At high concentrations, hydrodynam…
Previous particle-based computer simulations have revealed a significantly more pronounced tendency of spontaneous global polar ordering in puller (contractile) microswimmer suspensions than in pusher (extensile) suspensions. We here evaluate a microscopic statistical theory to investigate the emergence of such order through a linear instability of the disordered state. For this purpose, input concerning the orientation-dependent pair-distribution function is needed, and we discuss corresponding approaches, particularly a heuristic variant of the Percus test-particle method applied to active s…
We study self-diffusion and sedimentation in colloidal suspensions of nearly-hard spheres using the multiparticle collision dynamics simulation method for the solvent with a discrete mesh model for the colloidal particles (MD+MPCD). We cover colloid volume fractions from 0.01 to 0.40 and compare the MD+MPCD simulations to Brownian dynamics simulations with free-draining hydrodynamics (BD) as well as pairwise far-field hydrodynamics described using the Rotne--Prager--Yamakawa mobility tensor (BD+RPY). The dynamics in MD+MPCD suggest that the colloidal particles are only partially coupled to the…
We present a comprehensive computational study of the short-time transport properties of bidisperse neutral colloidal suspensions and the corresponding porous media. Our study covers bidisperse particle size ratios up to $4$, and total volume fractions up to and beyond the monodisperse hard-sphere close packing limit. The many-body hydrodynamic interactions are computed using conventional Stokesian Dynamics (SD) via a Monte-Carlo approach. We address suspension properties including the short-time translational and rotational self-diffusivities, the instantaneous sedimentation velocity, the wav…
Shear thickening is a widespread phenomenon in suspension flow that, despite sustained study, is still the subject of much debate. The longstanding view that shear thickening is due to hydrodynamic clusters has been challenged by recent theory and simulations suggesting that contact forces dominate, not only in discontinuous, but also in continuous shear thickening. Here, we settle this dispute using shear reversal experiments on micron-sized silica and latex colloidal particles to measure directly the hydrodynamic and contact force contributions to shear thickening. We find that contact force…
In order to asses the effect of hydrodynamics in the assembly of active attractive spheres, we simulate a semi-dilute suspension of attractive self-propelled spherical particles in a quasi two dimensional geometry comparing the case with and without hydrodynamics interactions. To start with, independently on the presence of hydrodynamics, we observe that depending on the ratio between attraction and propulsion, particles either coarsen or aggregate forming finite-size clusters. Focusing on the clustering regime, we characterize two different clusters parameters, i.e. their morphology and orien…
We utilize a generalized Irving-Kirkwood procedure to derive the hydrodynamic equations of an active matter suspension with internal structure and driven by internal torque. The internal structure and torque of the active Brownian particles give rise to a balance law for internal angular momentum density, making the hydrodynamic description a polar theory of continuum mechanics. We derive exact microscopic expressions for the stress tensor, couple stress tensor, internal energy density, and heat flux vector. Unlike passive matter, the symmetry of the stress tensor is broken explicitly due to a…
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 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 derive the hydrodynamic equations of motion for a fluid of active particles described by under- damped Langevin equations that reduce to the Active-Brownian-Particle model, in the overdamped limit. The contraction into the hydrodynamic description is performed by locally averaging the par- ticle dynamics with the non-equilibrium many-particle probability density, whose formal expression is found in the physically relevant limit of high-friction through a multiple-time-scale analysis. This approach permits to identify the conditions under which self-propulsion can be subsumed into the fluid …
We study in this work a steady shearing laminar flow with null heat flux (usually called "uniform shear flow") in a gas-solid suspension at low density. The solid particles are modeled as a gas of smooth hard spheres with inelastic collisions while the influence of the surrounding interstitial fluid on the dynamics of grains is modeled by means of a volume drag force, in the context of a rheological model for suspensions. The model is solved by means of three different but complementary routes, two of them being theoretical (Grad's moment method applied to the corresponding Boltzmann equation …
Using a fluid-particle dynamics approach, we numerically study the effects of hydrodynamic interactions on the collective dynamics of active suspensions within a simple model for bacterial motility: each microorganism is modeled as a stroke-averaged dumbbell swimmer with prescribed dipolar force pairs. Using both simulations and qualitative arguments, we show that, when the separation between swimmers is comparable to their size, the swimmers' motions are strongly affected by activity-induced hydrodynamic forces. To further understand these effects, we investigate semidilute suspensions of swi…
We describe and analyze CUDA simulations of hydrodynamic interactions in active dumbbell suspensions. GPU-based parallel computing enables us not only to study the time-resolved collective dynamics of up to a several hundred active dumbbell swimmers but also to test the accuracy of effective time-averaged models. Our numerical results suggest that the stroke-averaged model yields a relatively accurate description down to distances of only a few times the dumbbell's length. This is remarkable in view of the fact that the stroke-averaged model is based on a far-field expansion. Thus, our analysi…
It is intuitive that the diffusivity of an isolated particle differs from those in a monodisperse suspension, in which hydrodynamic interactions between the particles are operative. Batchelor (1976,1983) calculated how hydrodynamic interactions influenced the diffusivity of a dilute suspension of spherical particles and Russel et al.(1991), and Brady (1994) treated non-dilute (higher particle volume fraction) suspensions. Although most particles lack perfect sphericity, little is known about the effects of hydrodynamic interactions on the diffusivity of spheroidal particles, which are the simp…
Fluctuating hydrodynamics has been successfully combined with several computational methods to rapidly compute the correlated random velocities of Brownian particles. In the overdamped limit where both particle and fluid inertia are ignored, one must also account for a Brownian drift term in order to successfully update the particle positions. In this paper, we present an efficient computational method for the dynamic simulation of Brownian suspensions with fluctuating hydrodynamics that handles both computations and provides a similar approximation as Stokesian Dynamics for dilute and semidil…
At the surfaces of autophoretic colloids, slip velocities arise from local chemical gradients that are many-body functions of particle configuration and activity. For rapid chemical diffusion, coupled with slip-induced hydrodynamic interactions, we deduce the chemohydrodynamic forces and torques between colloids. Near a no-slip wall, the forces can be expressed as gradients of a non-equilibrium potential which, by tuning the type of activity, can be varied from repulsive to attractive. When this potential has a barrier, we find arrested phase separation with a mean cluster size set by competin…
We use shear reversal simulations to explore the rheology of dense, non-Brownian suspensions, resolving lubrication forces between neighbouring particles and modelling particle surface contacts. The transient stress response to an abrupt reversal of the direction of shear shows rate-independent, nonmonotonic behaviour, capturing the salient features of the corresponding classical experiments. Based on analyses of the hydrodynamic and particle contact stresses and related contact networks, we demonstrate distinct responses at small and large strains, associated with contact breakage and structu…
