Run-and-tumble particles with hydrodynamics: sedimentation, trapping, and upstream swimming

Artificial living crystals in confined environment

Similar to the spontaneous formation of colonies of bacteria, flocks of birds, or schools of fish, "living crystals" can be formed by artificial self-propelled particles such as Janus colloids. Unlike usual solids, these "crystals" are far from thermodynamic equilibrium. They fluctuate in time forming a crystalline structure, breaking apart and re-forming again. We propose a method to stabilize living crystals by applying a weak confinement potential that does not suppress the ability of the particles to perform self-propelled motion, but it stabilizes the structure and shape of the dynamical clusters. This gives rise to such configurations of living crystals as "living shells" formed by Janus colloids. Moreover, the shape of the stable living clusters can be controlled by tuning the potential strength. Our proposal can be verified experimentally with either artificial microswimmers such as Janus colloids, or with living active matter.

Lattice-Boltzmann simulations of microswimmer-tracer interactions

Hydrodynamic interactions in systems composed of self-propelled particles, such as swimming microorganisms and passive tracers, have a significant impact on the tracer dynamics compared to the equivalent "dry" sample. However, such interactions are often difficult to take into account in simulations due to their computational cost. Here, we perform a systematic investigation of swimmer-tracer interaction using an efficient force-counterforce-based lattice-Boltzmann (LB) algorithm [De Graaf et al., J. Chem. Phys. 144, 134106 (2016)JCPSA60021-960610.1063/1.4944962] in order to validate its ability to capture the relevant low-Reynolds-number physics. We show that the LB algorithm reproduces far-field theoretical results well, both in a system with periodic boundary conditions and in a spherical cavity with no-slip walls, for which we derive expressions here. The force-lattice coupling of the LB algorithm leads to a "smearing out" of the flow field, which strongly perturbs the tracer trajectories at close swimmer-tracer separations, and we analyze how this effect can be accurately captured using a simple renormalized hydrodynamic theory. Finally, we show that care must be taken when using LB algorithms to simulate systems of self-propelled particles, since its finite momentum transport time can lead to significant deviations from theoretical predictions based on Stokes flow. These insights should prove relevant to the future study of large-scale microswimmer suspensions using these methods.

Active Brownian particles and run-and-tumble particles separate inside a maze

A diverse range of natural and artificial self-propelled particles are known and are used nowadays. Among them, active Brownian particles (ABPs) and run-and-tumble particles (RTPs) are two important classes. We numerically study non-interacting ABPs and RTPs strongly confined to different maze geometries in two dimensions. We demonstrate that by means of geometrical confinement alone, ABPs are separable from RTPs. By investigating Matryoshka-like mazes with nested shells, we show that a circular maze has the best filtration efficiency. Results on the mean first-passage time reveal that ABPs escape faster from the center of the maze, while RTPs reach the center from the rim more easily. According to our simulations and a rate theory, which we developed, ABPs in steady state accumulate in the outermost region of the Matryoshka-like mazes, while RTPs occupy all locations within the maze with nearly equal probability. These results suggest a novel technique for separating different types of self-propelled particles by designing appropriate confining geometries without using chemical or biological agents.

Flow-induced nonequilibrium self-assembly in suspensions of stiff, apolar, active filaments

Active bodies in viscous fluids interact hydrodynamically through self-generated flows. A stiff, apolar, active filament generates symmetric fluid flow around it and thus cannot self-propel. Here we study the mobility and aggregation induced by hydrodynamic flow in a suspension of stiff, apolar, active filaments. We consider two types of active filaments, with those producing extensile or contractile flows along their long axis. Lateral hydrodynamic attractions in extensile filaments lead, independent of the volume fraction, to anisotropic aggregates which translate and rotate ballistically. Lateral hydrodynamic repulsions in contractile filaments lead to microstructured states, where the degree of clustering increases with the volume fraction and the filament motion is always diffusive. Our results demonstrate that the interplay between active hydrodynamic flows and anisotropic excluded volume interactions provides a generic nonequilibrium mechanism for hierarchical self-assembly of active soft matter.

Microfluidic rheology of active particle suspensions: Kinetic theory

We analyze the effective rheology of a dilute suspension of self-propelled slender particles confined between two infinite parallel plates and subject to a pressure-driven flow. We use a continuum kinetic model to describe the configuration of the particles in the system, in which the disturbance flows induced by the swimmers are taken into account, and use it to calculate estimates of the suspension viscosity for a range of channel widths and flow strengths typical of microfluidic experiments. Our results are in agreement with previous bulk models, and in particular, demonstrate that the effect of activity is strongest at low flow rates, where pushers tend to decrease the suspension viscosity whereas pullers enhance it. In stronger flows, dissipative stresses overcome the effects of activity leading to increased viscosities followed by shear-thinning. The effects of confinement and number density are also analyzed, and our results confirm the apparent transition to superfluidity reported in recent experiments on pusher suspensions at intermediate densities. We also derive an approximate analytical expression for the effective viscosity in the limit of weak flows and wide channels, and demonstrate good agreement between theory and numerical calculations.

Superdiffusion in dispersions of active colloids driven by an external field and their sedimentation equilibrium

The diffusive behaviors of active colloids with run-and-tumble movement are explored by dissipative particle dynamics simulations for self-propelled particles (force dipole) and external field-driven particles (point force). The self-diffusion of tracers (solvent) is investigated as well. The influences of the active force, run time, and concentration associated with active particles are studied. For the system of self-propelled particles, the normal diffusion is observed for both active particles and tracers. The diffusivity of the former is significantly greater than that of the latter. For the system of field-driven particles, the superdiffusion is seen for both active particles and tracers. In contrast, it is found that the anomalous diffusion exponent of the former is slightly less than that of the latter. The anomalous diffusion is caused by the many-body, long-range hydrodynamic interactions. In spite of the superdiffusion, the sedimentation equilibrium of field-driven particles can be acquired and the density profile is still exponentially decayed. The sedimentation length of field-driven particles is always greater than that of self-propelled particles.

Purely hydrodynamic origin for swarming of swimming particles

Three-dimensional simulations with fully resolved hydrodynamics are performed to study the collective motion of model swimmers in bulk and confinement. Calculating the dynamic structure factor, we clarified that the swarming in bulk systems can be understood as a pseudoacoustic mode. Under confinement between flat parallel walls, this pseudoacoustic mode leads to a traveling wavelike motion. This swarming behavior is due purely to the hydrodynamic interactions between the swimmers and depends strongly on the type and strength of swimming (i.e., pusher or puller).

Acoustic trapping of active matter

Confinement of living microorganisms and self-propelled particles by an external trap provides a means of analysing the motion and behaviour of active systems. Developing a tweezer with a trapping radius large compared with the swimmers' size and run length has been an experimental challenge, as standard optical traps are too weak. Here we report the novel use of an acoustic tweezer to confine self-propelled particles in two dimensions over distances large compared with the swimmers' run length. We develop a near-harmonic trap to demonstrate the crossover from weak confinement, where the probability density is Boltzmann-like, to strong confinement, where the density is peaked along the perimeter. At high concentrations the swimmers crystallize into a close-packed structure, which subsequently ‘explodes' as a travelling wave when the tweezer is turned off. The swimmers' confined motion provides a measurement of the swim pressure, a unique mechanical pressure exerted by self-propelled bodies.

Active matter, such as swimming bacteria, show unique behaviors under confinement, but it is experimentally challenging to measure them. Takatori et al. show the use of acoustic tweezers to trap self-propelled Janus particles as an enabling tool to investigate collective motions in living systems.

Upward swimming of a sperm cell in shear flow

Mammalian sperm cells are required to swim over long distances, typically around 1000-fold their own length. They must orient themselves and maintain a swimming motion to reach the ovum, or egg cell. Although the mechanism of long-distance navigation is still unclear, one possible mechanism, rheotaxis, was reported recently. This work investigates the mechanism of the rheotaxis in detail by simulating the motions of a sperm cell in shear flow adjacent to a flat surface. A phase diagram was developed to show the sperm's swimming motion under different shear rates, and for varying flagellum waveform conditions. The results showed that, under shear flow, the sperm is able to hydrodynamically change its swimming direction, allowing it to swim upwards against the flow, which suggests that the upward swimming of sperm cells can be explained using fluid mechanics, and this can then be used to further understand physiology of sperm cell navigation.

Collective Behavior of Quorum-Sensing Run-and-Tumble Particles under Confinement

We study a generic model for quorum-sensing bacteria in circular confinement. Every bacterium produces signaling molecules, the local concentration of which triggers a response when a certain threshold is reached. If this response lowers the motility, then an aggregation of bacteria occurs which differs fundamentally from standard motility-induced phase separation due to the long-ranged nature of the concentration of signal molecules. We analyze this phenomenon analytically and by numerical simulations employing two different protocols leading to stationary cluster and ring morphologies, respectively.

Getting drowned in a swirl: Deformable bead-spring model microswimmers in external flow fields

Deformability is a central feature of many types of microswimmers, e.g., for artificially generated self-propelled droplets. Here, we analyze deformable bead-spring microswimmers in an externally imposed solvent flow field as simple theoretical model systems. We focus on their behavior in a circular swirl flow in two spatial dimensions. Linear (straight) two-bead swimmers are found to circle around the swirl with a slight drift to the outside with increasing activity. In contrast to that, we observe for triangular three-bead or squarelike four-bead swimmers a tendency of being drawn into the swirl and finally getting drowned, although a radial inward component is absent in the flow field. During one cycle around the swirl, the self-propulsion direction of an active triangular or squarelike swimmer remains almost constant, while their orbits become deformed exhibiting an "egglike" shape. Over time, the swirl flow induces slight net rotations of these swimmer types, which leads to net rotations of the egg-shaped orbits. Interestingly, in certain cases, the orbital rotation changes sense when the swimmer approaches the flow singularity. Our predictions can be verified in real-space experiments on artificial microswimmers.

Effect of reorientation statistics on torque response of self-propelled particles

We consider the dynamics of self-propelled particles subject to external torques. Two models for the reorientation of self-propulsion are considered: run-and-tumble particles and active Brownian particles. Using the standard tools of nonequilibrium statistical mechanics we show that the run and tumble particles have a more robust response to torques. This macroscopic signature of the underlying reorientation statistics can be used to differentiate between the two types of self-propelled particles.

Rheotaxis of spherical active particles near a planar wall

For active particles the interplay between the self-generated hydrodynamic flow and an external shear flow, especially near bounding surfaces, can result in a rich behavior of the particles not easily foreseen from the consideration of the active and external driving mechanisms in isolation. For instance, under certain conditions, the particles exhibit "rheotaxis", i.e., they align their direction of motion with the plane of shear spanned by the direction of the flow and the normal of the bounding surface and move with or against the flow. To date, studies of rheotaxis have focused on elongated particles (e.g., spermatozoa), for which rheotaxis can be understood intuitively in terms of a "weather vane" mechanism. Here we investigate the possibility that spherical active particles, for which the "weather vane" mechanism is excluded due to the symmetry of the shape, may nevertheless exhibit rheotaxis. Combining analytical and numerical calculations, we show that, for a broad class of spherical active particles, rheotactic behavior may emerge via a mechanism which involves "self-trapping" near a hard wall owing to the active propulsion of the particles, combined with their rotation, alignment, and "locking" of the direction of motion into the shear plane. In this state, the particles move solely up- or downstream at a steady height and orientation.

Self-phoretic active particles interacting by diffusiophoresis: A numerical study of the collapsed state and dynamic clustering

Self-phoretic active colloids move and orient along self-generated chemical gradients by diffusiophoresis, a mechanism reminiscent of bacterial chemotaxis. In combination with the activity of the colloids, this creates effective repulsive and attractive interactions between particles depending on the sign of the translational and rotational diffusiophoretic parameters. A delicate balance of these interactions causes dynamic clustering and for overall strong effective attraction the particles collapse to one single cluster. Using Langevin dynamics simulations, we extend the state diagram of our earlier work (Phys. Rev. Lett. 112, 238303 (2014)) to regions with translational phoretic repulsion. With increasing repulsive strength, the collapsed cluster first starts to fluctuate strongly, then oscillates between a compact form and a colloidal cloud, and ultimately the colloidal cloud becomes static. The oscillations disappear if the phoretic interactions within compact clusters are not screened. We also study dynamic clustering at larger area fractions by exploiting cluster size distributions and mean cluster sizes. In particular, we identify the dynamic clustering 2 state as a signature of phoretic interactions. We analyze fusion and fission rate functions to quantify the kinetics of cluster formation and identify them as local signatures of phoretic interactions, since they can be measured on single clusters.

Physics of microswimmers--single particle motion and collective behavior: a review

Locomotion and transport of microorganisms in fluids is an essential aspect of life. Search for food, orientation toward light, spreading of off-spring, and the formation of colonies are only possible due to locomotion. Swimming at the microscale occurs at low Reynolds numbers, where fluid friction and viscosity dominates over inertia. Here, evolution achieved propulsion mechanisms, which overcome and even exploit drag. Prominent propulsion mechanisms are rotating helical flagella, exploited by many bacteria, and snake-like or whip-like motion of eukaryotic flagella, utilized by sperm and algae. For artificial microswimmers, alternative concepts to convert chemical energy or heat into directed motion can be employed, which are potentially more efficient. The dynamics of microswimmers comprises many facets, which are all required to achieve locomotion. In this article, we review the physics of locomotion of biological and synthetic microswimmers, and the collective behavior of their assemblies. Starting from individual microswimmers, we describe the various propulsion mechanism of biological and synthetic systems and address the hydrodynamic aspects of swimming. This comprises synchronization and the concerted beating of flagella and cilia. In addition, the swimming behavior next to surfaces is examined. Finally, collective and cooperate phenomena of various types of isotropic and anisotropic swimmers with and without hydrodynamic interactions are discussed.

Induced polar order in sedimentation equilibrium of rod-like nanoswimmers

The active diffusion and sedimentation equilibrium of rod-like nanoswimmers with length L are investigated by dissipative particle dynamics. In the absence of propulsion, the nanorod has the rotational correlation time τθ and mobility μ0, which vary with L. On the basis of the mean squared displacement, the diffusive behavior of rod-like nanoswimmers subject to active force Fa is found to follow (D - D0) ∝ (μ0Fa)(2)τθ, where D0 depicts the Brownian diffusivity. When the nanoswimmer suspension is under the external force Fe, the balance between the downward migration and upward active diffusion yields the sedimentation length δ = D/(μ0Fe), which no longer obeys δ0 = kBT/Fe obtained from the Einstein-Smoluchowski relationship, D0 = μ0kBT. Different from the suspension of passive rods, the polar order is clearly seen for active rods. The local polar order is essentially constant within the distance of about 2δ from the bottom wall but decays as the distance is further increased. In this work, the active Peclet number is small compared to unity and the maximum polar order grows linearly with Fe/Fa. The polar order arises because it is easier for the nanoswimmer with the swimming direction opposite to the external force to escape from the bottom wall.

Impact of hydrodynamics on effective interactions in suspensions of active and passive matter

Passive particles exhibit unique properties when immersed in an active bath of self-propelling entities. In particular, an effective attraction can appear between particles that repel each other when in a passive solution. Here we numerically study the effect of hydrodynamics on an active-passive hybrid system, where we observe qualitative differences as compared to simulations with excluded volume effects alone. The results shed light on an existing discrepancy in pair lifetimes between simulation and experiment, due to the hydrodynamically enhanced stability of coupled passive particles.

Dynamics and density distribution of strongly confined noninteracting nonaligning self-propelled particles in a nonconvex boundary

We study the dynamics of nonaligning, noninteracting self-propelled particles confined to a box in two dimensions. In the strong confinement limit, when the persistence length of the active particles is much larger than the size of the box, particles stay on the boundary and align with the local boundary normal. It is then possible to derive the steady-state density on the boundary for arbitrary box shapes. In nonconvex boxes, the nonuniqueness of the boundary normal results in hysteretic dynamics and the density is nonlocal, i.e., it depends on the global geometry of the box. These findings establish a general connection between the geometry of a confining box and the behavior of an ideal active gas it confines, thus providing a powerful tool to understand and design such confinements.

Segregation and phase inversion of strongly and weakly fluctuating Brownian particle mixtures and a chain of such particle mixtures in spherical containers

We investigate the segregation pattern formation of strongly and weakly fluctuating Brownian particle mixtures confined in a three-dimensional spherical container. We consider systems where the particle motion is restricted by the harmonic external trapping potential and the container edge wall. In such systems, two segregation patterns are observed. When the container radius is sufficiently large, more weakly fluctuating particles accumulate near the center of the container than strongly fluctuating particles. On the other hand, the distributions of the strongly and weakly fluctuating particles are inverted when the container radius is small. With no external trapping potentials, we find similar segregation and phase inversion if the particles construct a chain (heterofluctuating polymer) and are confined in a three-dimensional spherical container. We could apply these phenomena in the study of biopolymer behavior, such as chromosomes in the cell nucleus.

Dynamics of self-propelled particles under strong confinement

We develop a statistical theory for the dynamics of non-aligning, non-interacting self-propelled particles confined in a convex box in two dimensions. We find that when the size of the box is small compared to the persistence length of a particle's trajectory (strong confinement), the steady-state density is zero in the bulk and proportional to the local curvature on the boundary. Conversely, the theory may be used to construct the box shape that yields any desired density distribution on the boundary, thus offering a general tool to understand and design such confinements. When the curvature variations are small, we also predict the distribution of orientations at the boundary and the exponential decay of pressure as a function of box size recently observed in simulations in a spherical box.

Self-induced polar order of active Brownian particles in a harmonic trap

Hydrodynamically interacting active particles in an external harmonic potential form a self-assembled fluid pump at large enough Péclet numbers. Here, we give a quantitative criterion for the formation of the pump and show that particle orientations align in the self-induced flow field in surprising analogy to ferromagnetic order where the active Péclet number plays the role of inverse temperature. The particle orientations follow a Boltzmann distribution Φ(p) ∼ exp(Ap(z)) where the ordering mean field A scales with the active Péclet number and polar order parameter. The mean flow field in which the particles' swimming directions align corresponds to a regularized Stokeslet with strength proportional to swimming speed. Analytic mean-field results are compared with results from Brownian dynamics simulations with hydrodynamic interactions included and are found to capture the self-induced alignment very well.

Velocity alignment leads to high persistence in confined cells

Many cell types display random motility on two-dimensional substrates but crawl persistently in a single direction when confined in a microchannel or on an adhesive micropattern. Does this imply that the motility mechanism of confined cells is fundamentally different from that of unconfined cells? We argue that both free- and confined-cell migration may be described by a generic model of cells as "velocity-aligning" active Brownian particles previously proposed to solve a completely separate problem in collective cell migration. Our model can be mapped to a diffusive escape over a barrier and analytically solved to determine the cell's orientation distribution and repolarization rate. In quasi-one-dimensional confinement, velocity-aligning cells maintain their direction for times that can be exponentially larger than their persistence time in the absence of confinement. Our results suggest an important connection between single- and collective-cell migration: high persistence in confined cells corresponds with fast alignment of velocity to cell-cell forces.

Diffusion, sedimentation equilibrium, and harmonic trapping of run-and-tumble nanoswimmers

The diffusion of self-propelling nanoswimmers is explored by dissipative particle dynamics in which a nanoswimmer swims by forming an instantaneous force dipole with one of its nearest neighboring solvent beads. Our simulations mimic run-and-tumble behavior by letting the swimmer run for a time τ, then it randomly changes its direction for the next run period. Our simulations show that the swimming speed (ν(a)) of a nanoswimmer is proportional to the propulsion force and the mobility of a pusher is the same as that of a puller. The effective diffusivity is determined by three methods: mean squared displacement, velocity autocorrelation function, and sedimentation equilibrium. The active colloid undergoes directed propulsion at short time scales but changes to random motion at long time scales. The velocity autocorrelation function decreases with time and becomes zero beyond the run time. Under gravity, the concentration profile of active colloids follows Boltzmann distribution with a sedimentation length consistent with that acquired from the drift-diffusion equation. In our simulation, all three methods yield the same result, the effective diffusivity of an active colloid is the sum of the diffusivity of a passive colloid and ν(a)²τ/6. When the active colloids are confined by a harmonic well, they are trapped within a confinement length defined by the balance between the swimmer active force and restoring force of the well. When the confinement length is large compared to the run length, the stationary density profile follows the Boltzmann distribution. However, when the run length exceeds the confinement length, the density distribution is no longer described by Boltzmann distribution, instead we found a bimodal distribution.

Settled and unsettled issues in particle settling

Colloid sedimentation has played a seminal role in the development of statistical physics thanks to the celebrated experiments by Perrin, which provided a concrete demonstration of molecular reality and gave strong support to Einstein's theory of Brownian motion. This review, which mostly focuses on settling at low Peclét number, where Brownian fluctuations are dominant, aims to show that a lot more can be learnt both from the sedimentation equilibrium and from the particle settling dynamics of a wide class of systems, ranging from simple colloids to mesogenic suspensions, from soft solids to active particles and living organisms. At the same time, the occurrence of unexpected and surprising effects brings about challenging questions in statistical and fluid mechanics that make sedimentation an exciting field of research.

Cooperative roles of biological flow and surface topography in guiding sperm migration revealed by a microfluidic model

Successful reproduction in mammals requires sperm to swim against a fluid flow and through the long and complex female reproductive tract before reaching the egg in the oviduct. Millions of them do not make it. Despite their clinical importance, the roles played in sperm migration by the diverse biophysical and biochemical microenvironments within the reproductive tract are largely unknown. In this article, we present the development of a double layer microfluidic device that recreates two important biophysical environments within the female reproductive tract: fluid flow and surface topography. The unique feature of the device is that it enables one to study the cooperative roles of fluid flow and surface topography in guiding sperm migration. Using bull sperm as a model system, we found that microfluidic grooves embedded on a channel surface facilitate sperm migration against fluid flow. These findings suggest ways to design in vitro fertilization devices to treat infertility and to develop non-invasive contraceptives that use a microarchitectural design to entrap sperm.

Chaotic dynamics of a microswimmer in Poiseuille flow

The chaotic dynamics of pointlike, spherical particles in cylindrical Poiseuille flow is theoretically characterized and numerically confirmed when their own intrinsic swimming velocity undergoes temporal fluctuations around an average value. Two dimensionless ratios associated with the three significant temporal scales of the problem are identified that fully determine the chaos scenario. In particular, small but finite periodic fluctuations of swimming speed result in chaotic or regular motion depending on the position and orientation of the microswimmer with respect to the flow center line. Remarkably, the spatial extension of chaotic microswimmers is found to depend crucially on the fluctuations' period and amplitude and to be highly sensitive to the Fourier spectrum of the fluctuations. This has implications for the design of artificial microswimmers.

Periodic and quasiperiodic motion of an elongated microswimmer in Poiseuille flow

We study the dynamics of a prolate spheroidal microswimmer in Poiseuille flow for different flow geometries. When moving between two parallel plates or in a cylindrical microchannel, the swimmer performs either periodic swinging or periodic tumbling motion. Although the trajectories of spherical and elongated swimmers are qualitatively similar, the swinging and tumbling frequency strongly depends on the aspect ratio of the swimmer. In channels with reduced symmetry the swimmers perform quasiperiodic motion which we demonstrate explicitly for swimming in a channel with elliptical cross-section.

Autonomous motility of active filaments due to spontaneous flow-symmetry breaking

We simulate the nonlocal Stokesian hydrodynamics of an elastic filament which is active due a permanent distribution of stresslets along its contour. A bending instability of an initially straight filament spontaneously breaks flow symmetry and leads to autonomous filament motion which, depending on conformational symmetry, can be translational or rotational. At high ratios of activity to elasticity, the linear instability develops into nonlinear fluctuating states with large amplitude deformations. The dynamics of these states can be qualitatively understood as a superposition of translational and rotational motion associated with filament conformational modes of opposite symmetry. Our results can be tested in molecular-motor filament mixtures, synthetic chains of autocatalytic particles, or other linearly connected systems where chemical energy is converted to mechanical energy in a fluid environment.

Probability distributions for the run-and-tumble bacterial dynamics: an analogy to the Lorentz model

In this paper, we exploit an analogy of the run-and-tumble process for bacterial motility with the Lorentz model of electron conduction in order to obtain analytical results for the intermediate scattering function. This allows to obtain an analytical result for the van Hove function in real space for two-dimensional systems. We furthermore consider the 2D circling motion of bacteria close to solid boundaries with tumbling, and show that the analogy to electron conduction in a magnetic field allows to predict the effective diffusion coefficient of the bacteria. The latter is shown to be reduced by the circling motion of the bacteria.

Colloids in active fluids: anomalous microrheology and negative drag

We simulate an experiment in which a colloidal probe is pulled through an active nematic fluid. We find that the drag on the particle is non-stokesian (not proportional to its radius). Strikingly, a large enough particle in contractile fluid (such as an actomyosin gel) can show negative viscous drag in steady state: the particle moves in the opposite direction to the externally applied force. We explain this, and the qualitative trends seen in our simulations, in terms of the disruption of orientational order around the probe particle and the resulting modifications to the active stress.

Nonlinear dynamics of a microswimmer in Poiseuille flow

We study the three-dimensional dynamics of a spherical microswimmer in cylindrical Poiseuille flow which can be mapped onto a Hamiltonian system. Swinging and tumbling trajectories are identified. In 2D they are equivalent to oscillating and circling solutions of a mathematical pendulum. Hydrodynamic interactions between the swimmer and confining channel walls lead to dissipative dynamics and result in stable trajectories, different for pullers and pushers. We demonstrate this behavior in the dipole approximation of the swimmer and with simulations using the method of multiparticle collision dynamics.

Direct upstream motility in Escherichia coli

We provide an experimental demonstration of positive rheotaxis (rapid and continuous upstream motility) in wild-type Escherichia coli freely swimming over a surface. This hydrodynamic phenomenon is dominant below a critical shear rate and robust against Brownian motion and cell tumbling. We deduce that individual bacteria entering a flow system can rapidly migrate upstream (>20 μm/s) much faster than a gradually advancing biofilm. Given a bacterial population with a distribution of sizes and swim speeds, local shear rate near the surface determines the dominant hydrodynamic mode for motility, i.e., circular or random trajectories for low shear rates, positive rheotaxis for moderate flow, and sideways swimming at higher shear rates. Faster swimmers can move upstream more rapidly and at higher shear rates, as expected. Interestingly, we also find on average that both swim speed and upstream motility are independent of cell aspect ratio.

Diffusive transport without detailed balance in motile bacteria: does microbiology need statistical physics?

Microbiology is the science of microbes, particularly bacteria. Many bacteria are motile: they are capable of self-propulsion. Among these, a significant class execute so-called run-and-tumble motion: they follow a fairly straight path for a certain distance, then abruptly change direction before repeating the process. This dynamics has something in common with Brownian motion (it is diffusive at large scales), and also something in contrast. Specifically, motility parameters such as the run speed and tumble rate depend on the local environment and hence can vary in space. When they do so, even if a steady state is reached, this is not generally invariant under time reversal: the principle of detailed balance, which restores the microscopic time-reversal symmetry of systems in thermal equilibrium, is mesoscopically absent in motile bacteria. This lack of detailed balance (allowed by the flux of chemical energy that drives motility) creates pitfalls for the unwary modeller. Here I review some statistical-mechanical models for bacterial motility, presenting them as a paradigm for exploring diffusion without detailed balance. I also discuss the extent to which statistical physics is useful in understanding real or potential microbiological experiments.

Transport of self-propelling bacteria in micro-channel flow

Understanding the collective motion of self-propelling organisms in confined geometries, such as that of narrow channels, is of great theoretical and practical importance. By means of numerical simulations we study the motion of model bacteria in 2D channels under different flow conditions: fluid at rest, steady and unsteady flow. We find aggregation of bacteria near channel walls and, in the presence of external flow, also upstream swimming, which turns out to be a very robust result. Detailed analysis of bacterial velocity and orientation fields allows us to quantify the phenomenon by varying cell density, channel width and fluid velocity. The tumbling mechanism turns out to have strong influence on velocity profiles and particle flow, resulting in a net upstream flow in the case of non-tumbling organisms. Finally we demonstrate that upstream flow can be enhanced by a suitable choice of an unsteady flow pattern.

Theory of microbe motion in a poisoned environment

The motility of a microorganism which tries to avoid a poisoned environment by chemotaxis is studied within a simple model which couples its velocity to the concentration field of the poison. The latter is time independent but inhomogeneous in space. The presence of the poison is assumed to irreversibly reduce the propulsion speed. The model is solved analytically for different couplings of the total poison dose experienced by the microbe to the propulsion mechanism. In a stationary poison field resulting from a constant emission of a fixed point source, we find a power law for the distance traveled by the microbe as a function of time with a nonuniversal exponent which depends on the coupling in the model. With an inverted sign in the couplings, the acceleration of microbe motion induced by a food field can also be described.

Active colloidal suspensions exhibit polar order under gravity

Recently, the steady sedimentation profile of a dilute suspension of chemically powered colloids was studied experimentally [J. Palacci et al., Phys. Rev. Lett. 105, 088304 (2010)]. It was found that the sedimentation length increases quadratically with the swimming speed of the active Brownian particles. Here we investigate theoretically the sedimentation of self-propelled particles undergoing translational and rotational diffusion. We find that the measured increase of the sedimentation length is coupled to a partial alignment of the suspension with the mean swimming direction oriented against the gravitational field. We suggest realistic parameter values to observe this polar order. Furthermore, we find that the dynamics of the active suspension can be derived from a generalized free energy functional.

Nonlinear dynamics and rheology of active fluids: simulations in two dimensions

We report simulations of a continuum model for (apolar, flow aligning) active fluids in two dimensions. Both free and anchored boundary conditions are considered, at parallel confining walls that are either static or moving at fixed relative velocity. We focus on extensile materials and find that steady shear bands, previously shown to arise ubiquitously in one dimension for the active nematic phase at small (or indeed zero) shear rate, are generally replaced in two dimensions by more complex flow patterns that can be stationary, oscillatory, or apparently chaotic. The consequences of these flow patterns for time-averaged steady-state rheology are examined.

Sedimentation and effective temperature of active colloidal suspensions

In this Letter, we investigate experimentally the nonequilibrium steady state of an active colloidal suspension under gravity field. The active particles are made of chemically powered colloids, showing self propulsion in the presence of an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated microfluidic device, made of permeable gel microstructures. Both the microdynamics of individual colloids and the global stationary state of the suspension under gravity are measured with optical microscopy. This yields a direct measurement of the effective temperature of the active system as a function of the particle activity, on the basis of the fluctuation-dissipation relationship. Our work is a first step in the experimental exploration of the out-of-equilibrium properties of active colloidal systems.