Session D20: Active Matter in Complex Environments II

Polymers in Two-dimensional Bacterial Turbulence

In this talk, we experimentally investigate the effects of polymer additives on the collective dynamics of swarming Serratia marcescens in quasi-2D liquid films. We find that even minute amounts of polymers (< 20 ppm) can significantly enhance bacterial collective motion and promote large-scale coherent structures. Velocity statistics show that polymers reduce the likelihood of local velocity deviating from the mean swarming velocity, weakening the intermittency of fluctuations. Spatial and temporal correlations suggest that both the size and lifetime of flow structures are increased with polymers. In addition, we report an upscale transfer of enstrophy and energy using the recently developed filtering techniques. Unlike in classical 2D turbulence, both enstrophy and energy fluxes move primarily towards large scales in bacterial turbulence. The inverse enstrophy flux increases substantially with the addition of polymers, which is a potential mechanism for the increase in large-scale coherence.   

Crossing and non-crossing dictates the collective swimming of bacteria under two-dimensional confinement

The collective behavior of swimming bacteria in confined spaces, such as pores of the soil and interstices of tissues, is poorly understood. To study the effect of geometric confinement on bacterial collective behavior, we image a suspension of swimming Escherichia coli confined in a Hele-Shaw cell using bright-field microscopy. We find that the emergent collective phase formed by bacteria has two different symmetries depending on the gap thickness of the Hele-Shaw cell. For a gap thickness that is large enough to allow a pair of bacteria to cross over during a collision, the emergent collective phase exhibits long-range nematic order. In contrast, when bacteria are not able to cross over under stronger confinement, they assemble into transient clusters with short-range polar order. We explain the origin of these two different emergent symmetries by tracking the swimming behavior of individual bacteria in the two geometries with different gap thicknesses. Our experiments reveal the unusual dynamics of bacterial suspensions under geometric confinement and demonstrate a simple and effective way to control the emergent collective behavior of active matter.   

Play. Pause. Rewind. Measuring local entropy production and extractable work in active matter

Time-reversal symmetry breaking and entropy production are universal features of nonequilibrium phenomena. Despite its importance in the physics of active and living systems, the entropy production of systems with many degrees of freedom has remained of little practical significance because the high-dimensionality of their state space makes it difficult to measure. We introduce a local measure of entropy production and a numerical protocol to estimate it. We establish a connection between the entropy production and extractability of work in a given region of the system and show how this quantity depends crucially on the degrees of freedom being tracked. We validate our approach in theory, simulation, and experiments by considering systems of active Brownian particles undergoing motility induced phase separation, as well as active Brownian particles and E. Coli in a rectifying device in which the time-reversal asymmetry of the particle dynamics couples to spatial asymmetry to reveal its effects on a macroscopic scale.   

Rheotaxis of E.Coli in Viscoelastic Shear Thinning Fluids

The positive rheotaxis of microorganisms in Newtonian fluids encompasses the spontaneous orientation of individual swimmers against an unidirectional flow. This mechanism is now understood as being governed mainly by the positioning of the swimmer at an angle in the high shear flow region close to solid boundaries. Further studies underline a similar behavior for artificial self-propelled swimmers and demonstrates the hydrodynamic interplays that prescribes the swimmer’s gait.

 

Microorganisms have evolved to thrive in fluids that exhibit non-Newtonian behavior; these complex fluids are ubiquitous in nature and particularly in the human body. Our study focuses on the description of E. coli’s rheotaxis in Carbomethylcellulose and Xantham Gum solutions. Experiments and CFD simulations, show that the flux upstream is increased by an order of magnitude in viscoelastic shear-thinning fluids as opposed to strictly Newtonian viscous fluids. The analysis of E.Coli orientation distribution allows us to quantify the relative contribution of the elastic and viscous stresses on the phenomena.   

Active Transport of Particles within Biopolymer Solutions

The active motion of micro and nanometer-sized particles within complex fluids is relevant for a range of issues--including intracellular transport, navigation of viruses through mucus, and development of self-healing plastics. We integrated a standard optical microscope with a pair of coils, which can be used to create uniform magnetic field and field gradient. The set-up allows us to investigate both diffusion and directed motion of super-paramagnetic particles within polymer solutions and gels. The implementation of the platform and results from some of our preliminary experiments will be presented.   

Braiding Dynamics in Active Nematics

In active matter systems, energy consumed at the small scale by individual agents gives rise to emergent flows at large scales.  For 2D active nematic microtubule systems, these flows are largely characterized by the dynamics of mobile defects in the nematic director field.  As these defects wind about each other, their trajectories trace out braids, and the topological properties of these braids encode the most important global features of the flow.  In particular, the topological entropy of a braid quantifies how chaotic the associated flow is.  Since microtubule bundles, an extensile system, stretch out exponentially in time, the resultant defect movement must correspond to braids with positive topological entropy.  Indeed, we conjecture that the emergent defect dynamics are optimal in that they give braids which maximize the, suitably normalized, topological entropy.  In addition to the cases where the active nematic material is confined to a channel or the surface of a sphere, where there is good evidence for our conjecture, we share new experimental data concerning the behavior of microtubules confined to the region between a lattice of pillars.   

Confinement Effects on the Collective Behavior of Active Matter

Active colloidal matter can exhibit different collective phases in response to changes in the active particles' propulsion characteristics. Moreover, hydrodynamic interactions between colloidal particles and obstacles can also modulate their dynamics. The coupling between these two effects is not well understood, in part because resolving the hydrodynamic boundary conditions between many active colloids and many stationary obstacles is computationally very demanding. Only recently, the development of colloidal hydrodynamic simulation methods, such as the Smoothed Profile Method, have made this class of problems tractable. Using this method, we simulate dense active colloidal dispersions in strongly confined geometries and observe transitions in their collective behavior dependent on the interplay between the propulsion characteristics and the confinement.   

Weakly active particles near boundaries: towards solving the boundary value problem for active particles.

Boundaries play an important role in shaping the behavior of a system of active particles.  By considering the limit of noninteracting weakly-active Ornstein-Uhlenbeck particles, for which passive Brownian diffusion cannot be neglected and activity can be treated perturbatively, we develop a relatively simple expansion for the density of active particles in powers of the Peclet number and in terms of Hermite polynomials.  This approach allows us to cleanly formulate boundary conditions and study how active particles behave near boundaries in several different geometries: confinement by a single wall or between two walls in 1D, confinement in a circular or wedge-shaped region in 2D, motion near a corrugated or rough boundary, and absorption onto a sphere.  In this talk, we focus particularly on weakly active particles confined on a line and in a wedge-shaped region, and absorbing onto a sphere.  We discuss how quantites such as the pressure and flow of active particles changes as we gradually increase the activity away from a passive system.   

Novel Dynamical Features of Chiral Active Particles in Crowded Lattices

Active matter can convert ambient free energy into mechanical work at individual constituent level, giving rise to intriguing phenomena that far from equilibrium systems. On the one hand, chirality is ubiquitous in active matter; many biological and even synthetic active particles exhibit circular locomotion. On the other hand, a better understanding of how chiral active matter interact with complex environments can facilitate the applications of active matter. To this end, we perform particle-based simulations to investigate the transport properties of chiral active particles (CAPs) in a complex, crowded environment. Specifically, we use active Brownian dynamics to simulate CAPs self-propelling within a lattice of hard cylindrical obstacles. By tuning particle chirality and obstacle density, we identify a super-diffusion regime in which the CAPs become sensitive to the lattice configuration. We further study the transport of CAPs when subjected to a global flow. We predict a reentrant directional locking effect in that CAPs of high activities are directionally locked. As such, we demonstrate several novel dynamical features of CAPs that are not found in achiral active particles, paving the way towards designing chirality-based tools for single-cell diagnosis and separation.   

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We address the degeneracy of active flows in fluidic networks. 

Over the past decade, by engineering soft materials from active units, physicists have learned how to drive fluids from within. The generic strategy consists in assembling orientationally ordered liquids from self-propelled particles. Their resulting mesmerizing flows are now understood in basic geometries such as linear channels or circular chambers. However, unlike flows of Newtonian viscous fluids, active flows are intrinsically multistable. This strongly nonlinear behavior can result in highly degenerated flow patterns, even in simple geometries.

Building on model experiments based on Quincke roller fluids and minimal model simulations, we reveal and elucidate two qualitatively different classes of flow degeneracy when active fluids explore periodic lattices. Our work explains how the local strategies used by active flows to resolve geometrical frustration determine the large scale morphology of their flow fields.    

Doi-Peliti Field Theory of free Active Ornstein-Uhlenbeck Particles

We derive a Doi-Peliti field theory for free active Ornstein-Uhlenbeck particles, or, equivalently,

free inertial Brownian particles, and present a way to diagonalise the quadratic part of the action

and calculate the propagator. Unlike previous coarse-grained approaches this formulation correctly

tracks particle identity and yet can easily be expanded to include potentials and arbitrary reactions.   

Active Nematic Obstacle Courses

Active fluids, which spontaneously flow under their own internal energy, are commonly composed of nematic constituents, such as filamentous microtubules or rod-like bacteria. The activity and nematic elasticity generate a characteristic lengthscale that competes with any confining lengthscales. This competition of active length and confinement can lead to spatiotemporal ordered flow states, including vortex lattices and double helices in simple confining channels. Building upon recent work in confined active fluids, we employ a hybrid lattice Boltzmann and finite differences numerical solver to simulate an active nematic spontaneously flowing through an obstacle-laden channel. This geometry allows for an investigation of active nematic behaviour in heterogeneous environments. This talk will present our recent findings in channels with different obstacle configurations and imposed boundary conditions. We quantify the role that obstacle configuration can play in either stabilizing ordered flow states or aiding in the transition to disorderly active turbulence. Our numerical work will contribute to constructing a fundamental understanding of the relationship between biological active matter, such as bacterial colonies, and their complex surrounding environments   

Multiparticle collision dynamics simulations of squirmers in a nematic fluid

 We study the dynamics of a squirmer in a nematic liquid crystal using the multiparticle collision

dynamics (MPCD) method. A recently developed nematic MPCD method [Phys. Rev. E 99, 063319 (2019)]

which employs a tensor order parameter to describe the spatial and temporal variations of the nematic order

is used to simulate the suspending anisotropic fluid. Considering both nematodynamic effects (anisotropic

viscosity and elasticity) and thermal fluctuations, in the present study, we couple the nematic MPCD

algorithm with a molecular dynamics (MD) scheme for the squirmer. A unique feature of the proposed

method is that the nematic order, the fluid, and the squirmer are all represented in a particle-based

framework. To test the applicability of this nematic MPCD-MD method, we simulate the dynamics of a

spherical squirmer with homeotropic surface anchoring conditions in a bulk domain. The importance of

anisotropic viscosity and elasticity on the squirmer’s speed and orientation is studied for different values

of self-propulsion strength and squirmer type (pusher, puller or neutral). In sharp contrast to Newtonian

fluids, the speed of the squirmer in a nematic fluid depends on the squirmer type. Interestingly, the speed

of a strong pusher is smaller in the nematic fluid than for the Newtonian case. The orientational dynamics

of the squirmer in the nematic fluid also shows a non-trivial dependence on the squirmer type. Our results

compare well with existing experimental and numerical data. We also discuss early results on the dynamics of multiple squirmers in anisotropic fluids.   

Spontaneous rotation of polar active particles in a colloidal suspension

Polar active particles constitute a wide class of active matter that is able to propel along a preferential direction, given by their polar axis. Recent experiments and simulations showed that they can spontaneously break their polar symmetry and transition from a persistent Brownian motion with enhanced rotational diffusion to circular trajectories. Here, we demonstrate a generic active mechanism that leads to their spontaneous chiralization through a symmetry-breaking instability. We find that the transition of an active particle from a polar to a chiral symmetry is characterized by the emergence of active rotation and of circular trajectories. The instability is driven by the advection of a solute that interacts differently with the two portions of the particle surface and it occurs through a supercritical pitchfork bifurcation.   

Kelvin-Helmholtz Instability in Two Dimensional Semi-bounded Active Yukawa Liquids

Shear flows and the corresponding fluid instabilities are ubiquitous in nature - from astrophysical systems to bacterial dynamics. In a conventional medium, the free energy stored in the flow shear triggers a Kelvin-Helmholtz (KH) instability, which in turn grows and non-linearly saturates, leading to strong or weak turbulence.

In the present work, considering a two-dimensional semi-bounded cartesian domain, we systematically investigate the effect of activity, internal drives at the smallest scales of the system, on the growth, evolution, and saturation of KH instability, using Molecular Dynamics simulation[1], wherein a Yukawa liquid is used as a prototype. In particular, by increasing the percentage and the activity strength of the active particles, we demonstrate that activity increases the growth rate of the unstable spectrum[2]. Interestingly, it is found that the presence of activity not only alters the growth and the corresponding vortex dynamics, but also changes the bulk flow dynamics away from shear layers[2]. Our findings may have direct impact on a range of physics issues - from our understanding of biological active matter embedded in fluid flows to physics of mixing.