Bulletin of the American Physical Society
73rd Annual Meeting of the APS Division of Fluid Dynamics
Volume 65, Number 13
Sunday–Tuesday, November 22–24, 2020; Virtual, CT (Chicago time)
Session U03: Biological Fluid Dynamics: Locomotion Active Suspensions (8:45am  9:30am CST)Interactive On Demand

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U03.00001: Premelting controlled active matter in ice jeremy vachier, John Wettlaufer A collection of selfpropelled particles can undergo complex dynamics due to hydrodynamic and steric interactions. In the case of a foreign particle inside a subfreezing solid, such as a particle in ice, a premelted film forms around it allowing the particle to migrate under the influence of an external temperature gradient, which is a phenomenon called {\em thermal regelation}. It has recently been shown that the effect of biological impurities and their migration within an ice column can accelerate melting and migrate faster in turn. This is a positive feedback loop, where the ice melting initiates the migration of algae and diatoms, which also increases its melting. We have previously shown that the effect of regelation plays a major role in the migration of inert particles and impurities inside ice with important environmental implications. We recast this class of regelation phenomena in the stochastic framework of active Brownian dynamics. [Preview Abstract] 

U03.00002: Noisedriven aggregation of swimmers in the Kolmogorov flow Kyle Ferguson, Simon Berman, Kevin Mitchell, Tom Solomon We investigate theoretically the dynamics of ellipsoidal microswimmers in an externally imposed, laminar Kolmogorov flow. Through a phasespace analysis of the dynamics without noise, we find that swimmers favor either crossstream or rotational drift, depending on their swimming speed and aspect ratio. When including noise, i.e. rotational diffusion, Langevin simulations of our model show a transition from swimmer aggregation in lowshear regions of the flow to aggregation in highshear regions as the parameters are varied. We find that rotational diffusion tends to drive swimmers into certain parts of phase space. We characterize the dependence of this noisedriven phasespace aggregation on a swimmer’s speed, aspect ratio, and rotational diffusivity. The properties of the swimmer trajectories with noise explain the transition from highshear to lowshear aggregation. [Preview Abstract] 

U03.00003: Active mixing of swimming bacteria in a hyperbolic ﬂow Tom Solomon, John Buggeln, Simon Berman, Kevin Mitchell We present experiments on the motion of smoothswimming and tumbling bacillus subtilis bacteria in laminar ﬂows. For most of the experiments the ﬂow is a hyperbolic ﬂow in a PDMS, microﬂuidic cross channel cell. Since the bacteria are selfpropelled, they are able to swim across passive invariant manifolds that block the motion of passive tracers (including sessile bacteria). Theoretically, the motion of these active tracers is inﬂuenced by {\em swimming invariant manifolds} (SwIMs) that act as oneway barriers. We compare the motion of the trajectories to the SwIMs and their associated swimming ﬁxed points, as predicted by the theory. We also discuss the eﬀectiveness of the theory in explaining the behavior of tumbling bacteria. Time permitting, we will also present preliminary results for the motion of bacteria in a doublegyre (vortex) ﬂow. [Preview Abstract] 

U03.00004: Rotational and translational drag on a sphere in an active fluid Wan Luo, Robert Pelcovits, Thomas Powers We theoretically and computationally study the rotational and translational drag on a sphere in an active fluid. The active fluid is described by a hydrodynamic theory of active nematics in the isotropic phase. We solve the linearized steady state equations in three dimensions for the velocity and order parameter fields and find the torque on a rotating sphere and drag on a translating sphere. Working in the regime where the active fluid is stable, we find that for prolate active particles, activity helps the sphere to rotate or translate in extensile fluids but resists its rotation and translation in contractile fluids. For oblate active particles, activity leads to a resistive drag on a rotating or translating sphere in extensile fluids but helps the rotation and translation of a sphere in contractile fluids. When the size of the sphere is comparable to the correlation length, there is a nonNewtonian dependence of the effective shear viscosity on the radius of the sphere for both rotation and translation. Additionally, we see this effect for both the contractile and extensile cases. [Preview Abstract] 

U03.00005: Chaotic advection of microswimmers in the vortex lattice flow Simon Berman, Kevin Mitchell We investigate theoretically the chaotic trajectories of microswimmers in an externallydriven twodimensional vortex lattice flow. To this end, we generalize the invariant manifolds of passive advection by introducing swimming invariant manifolds (SwIMs), which govern the chaotic transport of swimmers. We use the geometry of the SwIMs to identify suitably defined oneway barriers to swimmers in physical space, which allow us to distinguish between qualitatively different swimmer trajectories in different parts of space. Lastly, we examine the interplay between the SwIMs and invariant tori that trap swimmers inside vortices. [Preview Abstract] 

U03.00006: Steadystate fluidflow established by active matterfluid interaction. Zijie Qu, Dominik Schildknecht, Jialong Jiang, Enrique Amaya, Shahriar Shadkhoo, HeunJin Lee, Tiffany Tsou, Tom Roeschinger, Jack Stellwagen, Nitzan Razin, Rob Phillips, David Van Valen, Matt Thomson Biological systems achieve precise control over ambient fluids by selforganizing active protein structures. Active structures consume chemical energy to generate mechanical stresses that induce organized fluid flows. Reconstitution of active matter driven fluid flows in vitro illuminates flowdominated biological processes. However, the mechanism of flow fields generated by the active structures remains poorly understood. Here, we apply an opticallycontrolled active matter system composed of microtubule filaments and kinesin motor proteins to analyze the persistent flow fields. We demonstrate that organized fluid flows emerge through dynamic feedback between microtubule network contractions and fluiddriven mass transport. The geometry of active stresses at the vertices of the microtubule network determines the architecture of induced flowfields allowing prediction of flow architecture given microtubule network geometry. Our work provides a foundation for programming microscopic fluidflows and could enable the engineering of versatile microfluidic devices. [Preview Abstract] 

U03.00007: Motion of an active particle in linear concentration gradients Prathmesh vinze, Akash Choudhary, Pushpavanam Subramaniam Janus particles are selfpropelling bodies which generate local concentration gradients in a thin layer ($\delta$) compared to the size ($a$) of the particle($\delta \ll a$). Chemical assymetry along the surface is essential to generate chemical gradients. This generated concentration gradient gives rise to diffusioosmotic flows in the thin layer which is equivalent to a slip when seen from far, resulting in swimming of the particle even without any external concentration gradient.In realistic situations Janus particles can be in a fluid with concentration gradients. Therefore, in this work, we theoretically study the effect of external linear concentration gradient(electrolytic and nonelectrolytic solutes) on Janus particle. The external gradient gives rise to a competition between the local concentration gradient and the external concentration gradient. We show that it can be captured by a nondimensional activity number.The framework is general for any arbritrary angle $\beta $ between the direction of concentration gradient and the axis of self propulsion. We see, for $\beta=0 $, only the translational velocity changes, subject to a change in strength of external concentration gradient. However, for other angles, the Janus particle undergoes rotation. [Preview Abstract] 

U03.00008: The role of inertia in active nematic turbulence ColinMarius Koch, Michael Wilczek Suspensions of active agents with nematic interactions can exhibit complex spatiotemporal dynamics such as mesoscale turbulence. Continuum descriptions for such systems are inspired by the hydrodynamic theory of liquid crystals and introduce additional effects of active stresses. The resulting equations feature an advective nonlinearity which represents inertial effects. The typically low Reynolds number of such active flows raises the question of the importance of the inertial effects. To address this question, we investigate mesoscale turbulence in a twodimensional dense suspension of active nematic liquid crystals. We compare numerical simulations with and without nonlinear advection of the flow field. We find that for sufficiently high activity, the simulations including nonlinear advection exhibit largescale motion which is not observed when excluding advection. Performing a spectral analysis of the energy budget, we identify an inverse energy transfer to the largest scales highlighting the importance of inertial effects in this model. We additionally show that surface friction, mimicked by a linear friction term, dissipates the transported energy and suppresses the largescale motion. [Preview Abstract] 

U03.00009: A computational method of optimizing slip velocities of microswimmers with arbitrary axisymmetric shapes Hanliang Guo, Hai Zhu, Ruowen Liu, Marc Bonnet, Shravan Veerapaneni This presentation discusses a computational approach to determine the optimal slip velocities on any given shape of an axisymmetric microswimmer suspended in a viscous fluid. The objective is to maximize the efficiency of the microswimmer, or equivalently to minimize the power loss to maintain a target swimming speed. We consider various families of shapes parameterized by the reduced volume and compute their swimming efficiency. In the case of timeindependent slip velocities, we show that, owing to the linearity of the Stokes equations governing the fluid motion, this PDEconstrained optimization problem can be reduced to a simpler quadratic optimization problem, which we solve using a highorder accurate boundary integral method. We found that for a given reduced volume, prolate spheroids are the most efficient microswimmer shapes. We proposed a shapebased scalar metric that is predictive on whether the optimal swimmer of a given shape is a pusher or puller without the need of performing the optimization. In the case of timedependent slip velocities, we observe metachronal waves as an effective way to propel the microswimmer. Effects of the shapes will also be discussed. [Preview Abstract] 

U03.00010: Defectmediated dynamics of coherent structures in active nematics Mattia Serra, Linnea Lemma, Luca Giomi, Zvonimir Dogic, Lakshminarayanan Mahadevan Cytoskeleton biopolymers, bacterial colonies, epithelial tissues and cell monolayers are examples of active nematics that display coordinated motion. Coherent motion in these systems is measured in terms of the global spatiotemporal organization of the orientational order parameter, and the local dynamics of nematic defects. But how are these coupled to the ambient velocity field that characterizes positional coherence? We combine dynamical systems theory, experiments on twodimensional motor protein mixtures, and simulations of nematodynamic models to show that active nematics also possess positional coherence. The presence of these can be measured using Coherent Structures (CSs)  Lagrangian attractors and repellers, invisible to Eulerian techniques and trajectory plots, and thus serve as the organizing skeletons of the underlying chaotic motion. To understand the interaction of positional and orientational coherence on the dynamics of defects, we then analyzed observations and simulations and see that $+$1/2 defects move and deform the attractors, which in turn shape particle motion. Additionally, we find that regions of $+$1/2 defects undergo high bending and low stretching/shearing deformations. We conclude with some consequences of our framework for multicellular tissues. [Preview Abstract] 

U03.00011: Structure and Dynamics of Disclination Loops and Lines in 3D Active Nematic Flows Daniel Beller, Guillaume Duclos, Raymond Adkins, Debarghya Banerjee, Matthew Peterson, Minu Varghese, Itamar Kolvin, Arvind Baskaran, Robert Pelcovits, Thomas Powers, Aparna Baskaran, Federico Toschi, Michael Hagan, Sebastian Streichan, Vincenzo Vitelli, Zvonimir Dogic Topological defects are essential to the chaotic selfstirring of active nematics, whose internally driven flows couple to orientational distortions. However, while the 2D case is wellstudied, in 3D the nematic topological defects become much more complex, including curvilinear disclinations of variable winding character. To understand 3D active nematic flow dynamics, we present calculations of active hydrodynamics with nematic elasticity, together with topological analysis of data from the first experiments on bulk 3D active nematics. We show that the dominant topological excitations are a certain geometrical family of topologically neutral closedloop disclinations, which move, deform, reconnect, and selfannihilate under the flow fields that they generate. [Preview Abstract] 

U03.00012: Bacterial fluid flows in thin spherical shells Jeremy Yodh, Shreyas Gokhale, Amit Nagarkar, L Mahadevan A dense suspension of motile bacteria confined to a plane can exhibit turbulentlike flow structures due to broken detailed balance at the bacterium scale.~ While bacterial turbulence has been experimentally studied in the plane, relatively little work has addressed~how swarming couples to more complex sample geometries.~ To explore this question, we confine dense suspensions of fluorescent~\textit{E. coli}~within the spherical shell of an oilbacteriaoil double emulsion, and we then image resultant bacterial fluid flows using confocal microscopy.~ By varying the radius of the double emulsion, we can explore how motile bacterial turbulence couples to curvature.~ Preliminary results suggest that the bacterial turbulence organizes into fluctuating~azimuthal flows, but more work is needed for corroboration of these results. This work is underway and will be reported.~ [Preview Abstract] 
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