Session S35: Active Matter: Collective Phenomena in Living Systems IV

Fluid flows created by swimming bacteria drive self-organization in confined suspensions

Concentrated suspensions of micro-swimmers can display intricate self-organized spatiotemporal patterns on scales larger than those of the individual motile units. The collective dynamics of swimming microorganisms exhibits a complex interplay with the surrounding fluid: the motile cells stir the fluid, which in turn can reorient and advect them. This feedback loop can result in long-range interactions between the cells. We present a computational model that takes into account these cell-fluid interactions and cell-cell forces and that predicts counterintuitive cellular order driven by long-range flows. The predictions are confirmed by new experiments with Bacillus Subtilis bacteria. Simulations and experiments show that if the micro-swimmers are confined inside thin cylindrical chambers the suspension self-organizes into a stable swirling vortex. If the micro-swimmers are confined in thin racetracks, a persistent unidirectional stream can emerge. Both these phenomena emerge as a result of the complex interplay between the swimmers, the specific confining boundaries and the fluid flow.   

Fluid flow in monolayers: Cells under pressure

Number density fluctuations are intimately tied to collective behavior in particulate soft matter and active matter systems, including tissue cell monolayers. In cell monolayers, there is no free space between cells, so density fluctuations must involve either out of plane motion, or cell volume fluctuations. Recent work has shown that cells fluctuate in volume to accommodate collective density fluctuations, and that fluid moves between cells in this process. However, measurements of the resistance to this flow with controlled applied pressures have never been performed. Here we apply pressure to local regions in cell monolayers with an indentation instrument mounted on an inverted microscope. While simultaneously measuring contact area, indentation depth, and applied force as a function of time we determine a compression modulus and a permeability of cells. We find that cells are highly permeable, and that cytoskeleton-generated stresses are large enough to drive fluid from cell to cell as they spontaneously fluctuate in volume.   

Hydrodynamic interactions and their role on the dynamics of bacterial predators.

We consider the effects of hydrodynamics on the behavior of bacterial predators searching for bacterial prey. Experimentally, we find that bacterial predators respond to external flow fields in addition to responding to their own self-generated flow fields neighboring surfaces and finite boundaries. We will discuss the implications of this finding on bacterial hunting strategies.   

Non-homogeneous flow profiles in sheared bacterial suspensions

Bacterial suspensions under shear exhibit interesting rheological behaviors including the remarkable “superfluidic” state with vanishing viscosity at low shear rates. Theoretical studies have shown that such “superfluidic” state is linked with non-homogeneous shear flows, which are induced by coupling between nematic order of active fluids and hydrodynamics of shear flows. However, although bulk rheology of bacterial suspensions has been experimentally studied, shear profiles within bacterial suspensions have not been explored so far. Here, we experimentally investigate the flow behaviors of E. coli suspensions under planar oscillatory shear. Using confocal microscopy and PIV, we measure velocity profiles across gap between two shear plates. We find that with increasing shear rates, high-concentration bacterial suspensions exhibit an array of non-homogeneous flow behaviors like yield-stress flows and shear banding. We show that these non-homogeneous flows are due to collective motion of bacterial suspensions. The phase diagram of sheared bacterial suspensions is systematically mapped as functions of shear rates an bacterial concentrations. Our experiments provide new insights into rheology of bacterial suspensions and shed light on shear induced dynamics of active fluids.   

Discontinuous fluidization transition in dense suspensions of actively deforming particles

Collective dynamics of self-propelled particles at high density have been shown to display a glass-like transition with a critical slowing down of 2 to 4 orders of magnitude. In this talk, we propose a new mechanism of injecting energy or activity via volume fluctuations. We show that the behaviour of actively deforming particles is strikingly different from that of self-propelled particles. In particular, we find a discontinuous non-equilibrium phase transition from a flowing state to an arrested state. Our minimal model might also explain the collective dynamics in epithelial tissues. In particular, without needing self-propulsion or cell-cell adhesion, volume fluctuations of individual cells alone might be sufficient to give rise to an active fluidization and collective dynamics in densely packed tissues.   

Superfluid-like dynamics in active vortex fluids

Active biological fluids exhibit rich non-equilibrium dynamics and share striking similarities with quantum fluids, from vortex formation and magnetic ordering to superfluid-like behavior. Building on universality ideas, we have recently proposed a generalization of the Navier--Stokes equations that captures qualitatively the active bulk flow structures observed in bacterial suspensions. Here, we present new numerical simulations that explicitly account for boundary and shear effects. The theory successfully reproduces recent experimental observations of bacterial suspensions, including a superfluid-like regime of nearly vanishing shear viscosity.~ Our simulations further predict a geometry-induced 'quantization' of viscosity and the existence of excited states capable of performing mechanical work. It is plausible that these results generalize to a broad a class of fluids that are subject to an active scale selection mechanism.   

Swarming in viscous fluids: three-dimensional patterns in swimmer- and force-induced flows

Mathematical models of self-propelled interacting particles have reproduced various fascinating ``swarming'' patterns observed in natural and artificial systems. The formulation of such models usually ignores the influence of the surrounding medium in which the particles swarm. Here we develop from first principles a three-dimensional theory of swarming particles in a viscous fluid environment and investigate how the hydrodynamic coupling among the particles may affect their collective behavior. Specifically, we examine the hydrodynamic coupling among self-propelled particles interacting through ``social'' or ``mechanical'' forces. We discover that new patterns arise as a consequence of different interactions and self-propulsion mechanisms. Examples include flocks with prolate or oblate shapes, intermittent mills, recirculating peloton-like structures, and jet-like fluid flows that kinetically destabilize mill-like structures. Our results reveal possible mechanisms for three-dimensional swarms to kinetically control their collective behaviors in fluids.   

Numerical study of the hydrodynamic interactions in an \textit{E-coli} suspension

The active suspension of \textit{E-coli} displays many interesting non-equilibrium phenomena, e.g. ``swarming'' at high bacteria concentrations, and viscosity change under simple shear. To understand the microscopic mechanism underlying these phenomena requires detailed knowledge about the hydrodynamics within the suspension. Here we numerically study in detail the hydrodynamic interactions between a bacterium and an ellipsoid tracer at small separations, where the tracer can no longer be treated as a point-like particle that creates no disturbance to local flow field. We observed a significant drop in bacterium swimming velocity, in agreement with previous experimental study.   

Anomalous diffusion of an ellipsoid in quasi-2D active fluids

Enhanced diffusion of a tracer particle is a unique feature in active fluids. Here, we studied the diffusion of an ellipsoid in a free-standing film of E. coli. Particle diffusion is linearly enhanced at low bacterial concentrations, whereas a non-linear enhancement is observed at high bacterial concentrations due to the giant fluctuation. More importantly, we uncover an anomalous coupling between the translational and rotational degrees of freedom that is strictly prohibited in the classical Brownian diffusion. Combining experiments with theoretical modeling, we show that such an anomaly arises from the stretching flow induced by the force dipole of swimming bacteria. Our work illustrates a novel universal feature of active matter and transforms the understanding of fundamental transport processes in microbiological systems.~~~~~~~~~   

Non-monotonic size-dependent particle diffusion in active fluids

We experimentally investigate the effect of particle size on the motion of passive polystyrene spheres in suspensions of Escherchia coli. Using particles covering a range of sizes from 0.6 to 39 microns, we probe particle dynamics at both short and long time scales. In all cases, the particles exhibit super-diffusive ballistic behavior at short times before eventually transitioning to diffusive behavior. Surprisingly, the long-time hydrodynamic effective diffusivity exhibits a peak in particle size; an anomalous response that is fundamentally different from classical thermal diffusion. Consistent with recent theory, we find that the active contribution to particle diffusion is controlled by a dimensionless parameter, the Peclet number. We propose a minimal model that allows us to predict the requirements for a peak in the diffusivity as well as the magnitude of the peak as a function of particle size and bacterial concentration. Our results have broad implications on characterizing active fluids using concepts drawn from classical thermodynamics.   

Hydrodynamics of spinning bacteria at a surface

Bacteria tethered to a surface by their flagellum show a variety of different spinning behaviors, including different angles made with the surface and rotation velocities. We have developed a hydrodynamic model to show that the different behaviors arise from several factors including the degree of flagellar constraint, the shape of the bacterium, the flexibility of the flagellar hook and the motor torque. Our minimal model produces the wide variety of behaviors observed in experiments and successfully predicts the detachment angle for bacteria with three different body curvatures.   

Mobile wedges in an active turbulent bath

The motion of micro-wedges in a turbulent bacterial bath is explored using computer simulations with explicit modeling of the bacteria and experiments. We demonstrate that collective turbulentlike motion in a bacterial bath can power and steer the directed transport of mesoscopic carriers through the suspension. We will show that both polar ordering and swirl shielding inside the wedge yield an optimal transport velocity. Finally, we show the behavior of several wedges exposed to a bacterial bath.   

Entrainment dominates the interaction of microalgae with micron-sized objects

Swimming microorganisms usually navigate through fluids containing a variety of microparticles, with which they inevitably interact with important biological and ecological implications. Regarding the prokaryotic realm, it has been shown that the colloidal dynamics within bacterial suspensions is well described by a persistent random walk. As to the other major class of microorganisms, the eukaryotes, much less is known. By directly tracking polystyrene colloids in baths of the model puller-type alga Chlamydomonas reinhardtii, a pioneering work [1] has shown that they still behave diffusively asymptotically with diffusivities linearly increasing with the concentration. The values reported as well as the distribution of displacements having exponential tails are well explained theoretically when considering the hydrodynamic far-field contribution of the algae. However nothing has yet been described regarding the short range interactions that inevitably exist. In this work we show, by means of 3 different experiments, that the coarse-grained dynamics of the colloids is in fact dominated by very rare but large jumps due to entrainment by the algae leading to a total effective diffusion an order of magnitude higher than previously reported. [1] Leptos et al, PRL 103, 198103 (2009).