Hotspots of boundary accumulation: dynamics and statistics of micro-swimmers in flowing films

Adaptive behaviors of planktonic Pseudomonas aeruginosa in response to the surface-deposited dead siblings

In this study, the 3D motion behaviors and the underlying adaptation mechanism of planktonic Pseudomonas aeruginosa (PAO1) in response to the deposited dead siblings nearby were explored. Utilizing a real-time 3D tracking technique, digital holographic microscopy (DHM), we demonstrate that planktonic cells near the surface covered with dead siblings have a lower density and a reduced 3D velocity compared with those upon viable ones. As a sign of chemosensory responses, bacteria swimming near the dead siblings exhibit increase in frequency of the 'flick' motion. Transcriptomic analysis by RNA-seq reveals an upregulated expression of dgcM and dgcE inhibited the movement of PAO1, accompanied by increased transcriptional levels of the virulence factor-related genes hcp1, clpV1, and vgrG1. Moreover, the decrease in l-glutamate and the increase in succinic acid in the metabolites of the dead bacteria layer promote the dispersion of planktonic bacteria. As a result, the dead siblings on a surface inhibit the bacterial accumulation and activate the adaptive defensive responses of planktonic PAO1 in the vicinity.

Active dipolar spheroids in shear flow and transverse field: Population splitting, cross-stream migration, and orientational pinning

We study the steady-state behavior of active, dipolar, Brownian spheroids in a planar channel subjected to an imposed Couette flow and an external transverse field, applied in the "downward" normal-to-flow direction. The field-induced torque on active spheroids (swimmers) is taken to be of magnetic form by assuming that they have a permanent magnetic dipole moment, pointing along their self-propulsion (swim) direction. Using a continuum approach, we show that a host of behaviors emerges over the parameter space spanned by the particle aspect ratio, self-propulsion and shear/field strengths, and the channel width. The cross-stream migration of the model swimmers is shown to involve a regime of linear response (quantified by a linear-response factor) in weak fields. For prolate swimmers, the weak-field behavior crosses over to a regime of full swimmer migration to the bottom half of the channel in strong fields. For oblate swimmers, a counterintuitive regime of reverse migration arises in intermediate fields, where a macroscopic fraction of swimmers reorient and swim to the top channel half at an acute "upward" angle relative to the field axis. The diverse behaviors reported here are analyzed based on the shear-induced population splitting (bimodality) of the swim orientation, giving two distinct, oppositely polarized, swimmer subpopulations (albeit very differently for prolate/oblate swimmers) in each channel half. In strong fields, swimmers of both types exhibit net upstream currents relative to the laboratory frame. The onsets of full migration and net upstream current depend on the aspect ratio, enabling efficient particle separation strategies in microfluidic setups.

Biofilms at interfaces: microbial distribution in floating films

Cellular motility is a key function guiding microbial adhesion to interfaces, which is the first step in the formation of biofilms. The close association of biofilms and bioremediation has prompted extensive research aimed at comprehending the physics of microbial locomotion near interfaces. We study the dynamics and statistics of microorganisms in a 'floating biofilm', i.e., a confinement with an air-liquid interface on one side and a liquid-liquid interface on the other. We use a very general mathematical model, based on a multipole representation and probabilistic simulations, to ascertain the spatial distribution of microorganisms in films of different viscosities. Our results reveal that microorganisms can be distributed symmetrically or asymmetrically across the height of the film, depending on their morphology and the ratio of the film's viscosity to that of the fluid substrate. Long-flagellated, elongated bacteria exhibit stable swimming parallel to the liquid-liquid interface when the bacterial film is less viscous than the underlying fluid. Bacteria with shorter flagella on the other hand, swim away from the liquid-liquid interface and accumulate at the free surface. We also analyze microorganism dynamics in a flowing film and show how a microorganism's ability to resist 'flow-induced-erosion' from interfaces is affected by its elongation and mode of propulsion. Our study generalizes past efforts on understanding microorganism dynamics under confinement by interfaces and provides key insights on biofilm initiation at liquid-liquid interfaces.

Oscillatory surface rheotaxis of swimming E. coli bacteria

Bacterial contamination of biological channels, catheters or water resources is a major threat to public health, which can be amplified by the ability of bacteria to swim upstream. The mechanisms of this 'rheotaxis', the reorientation with respect to flow gradients, are still poorly understood. Here, we follow individual E. coli bacteria swimming at surfaces under shear flow using 3D Lagrangian tracking and fluorescent flagellar labelling. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A theoretical analysis explains these rheotaxis regimes and predicts the corresponding critical shear rates. Our results shed light on bacterial transport and reveal strategies for contamination prevention, rheotactic cell sorting, and microswimmer navigation in complex flow environments.

Nutrient Transport Driven by Microbial Active Carpets

We demonstrate that active carpets of bacteria or self-propelled colloids generate coherent flows towards the substrate, and propose that these currents provide efficient pathways to replenish nutrients that feed back into activity. A full theory is developed in terms of gradients in the active matter density and velocity, and applied to bacterial turbulence, topological defects and clustering. Currents with complex spatiotemporal patterns are obtained, which are tunable through confinement. Our findings show that diversity in carpet architecture is essential to maintain biofunctionality.

State diagram of a three-sphere microswimmer in a channel

Geometric confinements are frequently encountered in soft matter systems and in particular significantly alter the dynamics of swimming microorganisms in viscous media. Surface-related effects on the motility of microswimmers can lead to important consequences in a large number of biological systems, such as biofilm formation, bacterial adhesion and microbial activity. On the basis of low-Reynolds-number hydrodynamics, we explore the state diagram of a three-sphere microswimmer under channel confinement in a slit geometry and fully characterize the swimming behavior and trajectories for neutral swimmers, puller- and pusher-type swimmers. While pushers always end up trapped at the channel walls, neutral swimmers and pullers may further perform a gliding motion and maintain a stable navigation along the channel. We find that the resulting dynamical system exhibits a supercritical pitchfork bifurcation in which swimming in the mid-plane becomes unstable beyond a transition channel height while two new stable limit cycles or fixed points that are symmetrically disposed with respect to the channel mid-height emerge. Additionally, we show that an accurate description of the averaged swimming velocity and rotation rate in a channel can be captured analytically using the method of hydrodynamic images, provided that the swimmer size is much smaller than the channel height.

Active fluids at circular boundaries: swim pressure and anomalous droplet ripening

We investigate the swim pressure exerted by non-chiral and chiral active particles on convex or concave circular boundaries. Active particles are modeled as non-interacting and non-aligning self-propelled Brownian particles. The convex and concave circular boundaries are used to model a fixed inclusion immersed in an active bath and a cavity (or container) enclosing the active particles, respectively. We first present a detailed analysis of the role of convex versus concave boundary curvature and of the chirality of active particles in their spatial distribution, chirality-induced currents, and the swim pressure they exert on the bounding surfaces. The results will then be used to predict the mechanical equilibria of suspended fluid enclosures (generically referred to as 'droplets') in a bulk with active particles being present either inside the bulk fluid or within the suspended droplets. We show that, while droplets containing active particles behave in accordance with standard capillary paradigms when suspended in a normal bulk, those containing a normal fluid exhibit anomalous behaviors when suspended in an active bulk. In the latter case, the excess swim pressure results in non-monotonic dependence of the inside droplet pressure on the droplet radius; hence, revealing an anomalous regime of behavior beyond a threshold radius, in which the inside droplet pressure increases upon increasing the droplet size. Furthermore, for two interconnected droplets, mechanical equilibrium can occur also when the droplets have different sizes. We thus identify a regime of anomalous droplet ripening, where two unequal-sized droplets can reach a final state of equal size upon interconnection, in stark contrast with the standard Ostwald ripening phenomenon, implying shrinkage of the smaller droplet in favor of the larger one.

Confined Flow: Consequences and Implications for Bacteria and Biofilms

Bacteria overwhelmingly live in geometrically confined habitats that feature small pores or cavities, narrow channels, or nearby interfaces. Fluid flows through these confined habitats are ubiquitous in both natural and artificial environments colonized by bacteria. Moreover, these flows occur on time and length scales comparable to those associated with motility of bacteria and with the formation and growth of biofilms, which are surface-associated communities that house the vast majority of bacteria to protect them from host and environmental stresses. This review describes the emerging understanding of how flow near surfaces and within channels and pores alters physical processes that control how bacteria disperse, attach to surfaces, and form biofilms. This understanding will inform the development and deployment of technologies for drug delivery, water treatment, and antifouling coatings and guide the structuring of bacterial consortia for production of chemicals and pharmaceuticals.

Re-entrant bimodality in spheroidal chiral swimmers in shear flow

We use a continuum model to report on the behavior of a dilute suspension of chiral swimmers subject to externally imposed shear in a planar channel. Swimmer orientation in response to the imposed shear can be characterized by two distinct phases of behavior, corresponding to unimodal or bimodal distribution functions for swimmer orientation along the channel. These phases indicate the occurrence (or not) of a population splitting phenomenon changing the swimming direction of a macroscopic fraction of active particles to the exact opposite of that dictated by the imposed flow. We present a detailed quantitative analysis elucidating the complexities added to the population splitting behavior of swimmers when they are chiral. In particular, the transition from unimodal to bimodal and vice versa are shown to display a re-entrant behavior across the parameter space spanned by varying the chiral angular speed. We also present the notable effects of particle aspect ratio and self-propulsion speed on system phase behavior and discuss potential implications of our results in applications such as swimmer separation/sorting.

Swimming and rafting of E.coli microcolonies at air-liquid interfaces

The dynamics of swimming microorganisms is strongly affected by solid‐liquid and air‐liquid interfaces. In this paper, we characterize the motion of both single bacteria and microcolonies at an air‐liquid interface. Both of them follow circular trajectories. Single bacteria preferentially show a counter‐clockwise motion, in agreement with previous experimental and theoretical findings. Instead, no preferential rotation direction is observed for microcolonies suggesting that their motion is due to a different physical mechanism. We propose a simple mechanical model where the microcolonies move like rafts constrained to the air‐liquid interface. Finally, we observed that the microcolony growth is due to the aggregation of colliding single‐swimmers, suggesting that the microcolony formation resembles a condensation process where the first nucleus originates by the collision between two single‐swimmers. Implications of microcolony splitting and aggregation on biofilm growth and dispersion at air‐liquid interface are discussed.

Diffusivity of E. coli-like microswimmers in confined geometries: The role of the tumbling rate

We analyzed the effect of confinement on the effective diffusion of a run-and-tumble E. coli-like flagellated microswimmer. We used a simulation protocol where the run phases are obtained via a fully resolved swimming problem, i.e., Stokes equations for the fluid coupled with rigid-body dynamics for the microorganism, while tumbles and collisions with the walls are modeled as random reorientation of the microswimmer. For weak confinement, the swimmer is trapped in circular orbits close to the solid walls. In this case, optimal diffusivity is observed when the tumbling frequency is comparable with the angular velocity of the stable orbits. For strong confinement, stable circular orbits disappear and the diffusion coefficient monotonically decreases with the tumbling rate. Our findings are generic and can be potentially applied to other natural or artificial chiral microswimmers that follow circular trajectories close to an interface or in confined geometries.

Wetting Transitions Displayed by Persistent Active Particles

A lattice model for active matter is studied numerically, showing that it displays wetting transitions between three distinctive phases when in contact with an impenetrable wall. The particles in the model move persistently, tumbling with a small rate α, and interact via exclusion volume only. When increasing the tumbling rates α, the system transits from total wetting to partial wetting and unwetting phases. In the first phase, a wetting film covers the wall, with increasing heights when α is reduced. The second phase is characterized by wetting droplets on the wall with a periodic spacing between them. Finally, the wall dries with few particles in contact with it. These phases present nonequilibrium transitions. The first transition, from partial to total wetting, is continuous and the fraction of dry sites vanishes continuously when decreasing the tumbling rate α. For the second transition, from partial wetting to dry, the mean droplet distance diverges logarithmically when approaching the critical tumbling rate, with saturation due to finite-size effects.

Population splitting of rodlike swimmers in Couette flow

We present a quantitative analysis on the response of a dilute active suspension of self-propelled rods (swimmers) in a planar channel subjected to an imposed shear flow. To best capture the salient features of the shear-induced effects, we consider the case of an imposed Couette flow, providing a constant shear rate across the channel. We argue that the steady-state behavior of swimmers can be understood in the light of a population splitting phenomenon, occurring as the shear rate exceeds a certain threshold, initiating the reversal of the swimming direction for a finite fraction of swimmers from down- to upstream or vice versa, depending on the swimmer position within the channel. Swimmers thus split into two distinct, statistically significant and oppositely swimming majority and minority populations. The onset of population splitting translates into a transition from a self-propulsion-dominated regime to a shear-dominated regime, corresponding to a unimodal-to-bimodal change in the probability distribution function of the swimmer orientation. We present a phase diagram in terms of the swim and flow Péclet numbers showing the separation of these two regimes by a discontinuous transition line. Our results shed further light on the behavior of swimmers in a shear flow and provide an explanation for the previously reported non-monotonic behavior of the mean, near-wall, parallel-to-flow orientation of swimmers with increasing shear strength.

Understanding the onset of oscillatory swimming in microchannels

Self-propelled colloids (swimmers) in confining geometries follow trajectories determined by hydrodynamic interactions with the bounding surfaces. However, typically these interactions are ignored or truncated to the lowest order. We demonstrate that higher-order hydrodynamic moments cause rod-like swimmers to follow oscillatory trajectories in quiescent fluid between two parallel plates, using a combination of lattice-Boltzmann simulations and far-field calculations. This behavior occurs even far from the confining walls and does not require lubrication results. We show that a swimmer's hydrodynamic quadrupole moment is crucial to the onset of the oscillatory trajectories. This insight allows us to develop a simple model for the dynamics near the channel center based on these higher hydrodynamic moments, and suggests opportunities for trajectory-based experimental characterization of swimmers' hydrodynamic properties.