Bulletin of the American Physical Society
75th Annual Meeting of the Division of Fluid Dynamics
Volume 67, Number 19
Sunday–Tuesday, November 20–22, 2022; Indiana Convention Center, Indianapolis, Indiana.
Session J04: Active Matter II: Active and Passive in Confinement |
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Chair: Spencer Smith, Mount Holyoke College Room: 131 |
Sunday, November 20, 2022 4:35PM - 4:48PM |
J04.00001: Passive and active particles in a lattice of obstacles Jean-Luc Thiffeault, Hongfei Chen Microswimmers and passive particles frequently encounter obstacles that slow down their progress. We consider a regular lattice of small obstacles, with which the particles interact only sterically. A natural question is: as they bounce around the lattice, what is the effective diffusion coefficient for the particles? We show that Brownian passive particles obey the same equation as for Rayleigh's problem of conduction in a perforated solid, with a similar solution in terms of reflections. For active particles, a homogenization approach involves a novel cell problem with boundary layers around columnar obstacles. |
Sunday, November 20, 2022 4:48PM - 5:01PM |
J04.00002: A simple catch: thermal fluctuations enable hydrodynamic trapping of microrollers by obstacles Michelle R Driscoll, Ernest B van der Wee, Blaise Delmotte, Brendan C Blackwell, Florencio Balboa Usabiaga, Andrey Sokolov, Isaiah Katz In order to leverage colloidal swimmers in microfluidic applications, it is crucial to understand their interaction with surface features such as obstacles. Previous studies have shown that this interaction can result in the hydrodynamic trapping, where the trapping strength heavily depends on the flow field of the swimmer, and that (thermal) noise is needed to escape the trap. Here, we use both experiments and simulations to investigate the interaction of driven microrollers with an obstacle. Microrollers have a prescribed propulsion direction and the flow field that drives their motion is quite different from previously-studied, bacteria-like or phoretic swimmers. We observe hydrodynamic trapping in our system, and find that the strength of the trap is controlled by obstacle curvature and repulsive potential. We detail the mechanisms of the trapping and find two remarkable features: it only happens in the wake of the obstacle and, more importantly, it can only occur with Brownian motion. While noise is usually needed to escape traps in dynamical systems, here we show it is the only means to reach a hydrodynamic attractor. Our findings indicate that while hydrodynamic trapping of microswimmers by obstacles is generic, thermal fluctuations can play an unexpected role. |
Sunday, November 20, 2022 5:01PM - 5:14PM |
J04.00003: Confined squirmers: interactions, contacts and clusters. Albane Thery, Eric Lauga The hydrodynamic squirmer model has been used as a proxy to understand the dynamics of microswimmers with diverse propulsion mechanisms, ranging from the beating of biological cilia to artificial chemical or phoretic actuation. When confined, a suspension of such swimmers exhibits collective properties, e.g. the clustering of Marangoni droplets above a wall. Here, we investigate the extent to which hydrodynamics, as opposed to other mechanisms, control these interactions. We first consider theoretically the symmetric boundary-mediated encounters of model microswimmers under gravity through the far-field interaction of a pair of weak squirmers. The behaviour of the swimmers is set by their orientation, itself controlled by the squirming parameters, which distinguishes pullers from pushers. We find that close to walls, contacts are unavoidable and that the interactions are then dominated by the dynamics after contact. We therefore focus on the near-field stability of groups of squirmers. Considering for simplicity a circular assembly, we can determine analytically the stability conditions for the clusters. Our simplified approach to active clustering enables us to highlight the hydrodynamic contribution to the dynamics, which can be otherwise hard to isolate in large-scale suspension simulations. |
Sunday, November 20, 2022 5:14PM - 5:27PM |
J04.00004: Active Nematics Confined by Pillar Arrays Spencer A Smith, Dimitrius A Khaladj In active nematic microtubule (ANMT) systems, extensile dynamics at the scale of microtubule bundles lead to interesting coherent flows at large scales. For 2D ANMT systems, these flows are largely characterized by the dynamics of mobile, topologically-protected defects in the nematic director field. When confined to simple geometries, such as channels or the surface of a sphere, the positive defects move according to specific braiding patterns, which can be predicted from recent ideas in braid theory and dynamical systems theory. Motivated by these predictions for a doubly periodic domain, we consider the behavior of ANMTs confined to the space between a square array of pillars. We share the results of recent experiments using this domain geometry. In particular, we will consider the interesting transport behavior of defects that emerges due to the pillar array, and see if any evidence for the predicted braiding pattern exists. |
Sunday, November 20, 2022 5:27PM - 5:40PM |
J04.00005: The Dynamics of a Circular Object Immersed In A Confined Active Suspension Jonathan B Freund Numerical simulations in two space dimensions are used to examine the dynamics, transport, and equilibrium behaviors of a free-floating circular object immersed in an active suspension within a closed container with fixed walls. The continuum model of Gao et al. (Phys. Rev. Fluids, 2017) is used to represent the suspension, which models non-interacting, immotile, extensor-type microscopic agents that have a direction and strength and an established quasi-nonequilibrium fourth-moment closure model. Such a suspension is well-known to be unstable above a threshold activity level that depends upon the length scale of the confinement. Introducing the free-floating object leads to additional phenomenology. Its presence can effectively confine nearby fluid, which can in turn suppress local suspension activity. However, as a rigid body, the object's motion also tends to correlate strains near its surface, which in turn correlates the activity and its net effect on induced stresses. For different activity levels and geometries, these mechanisms can lead to either an effective attraction toward or repulsion away from fixed no-slip wall boundaries. In addition, a curious propagating behavior is found for some conditions when the object is near a wall boundary, which provides a potential mechanism for long-range transport. |
Sunday, November 20, 2022 5:40PM - 5:53PM |
J04.00006: Dispersion of passive colloids suspended in an active suspension Tanumoy Dhar, David Saintillan We study the transport of passive colloids immersed in a bath of non-interacting run-and-tumble microswimmers using a minimal model for colloid-swimmer interactions. Stochastic simulations are employed to estimate the effective diffusivity of a single suspended colloid, which we estimate in terms of the relevant non-dimensional groups, namely the ratio of the swimmer persistence length to the colloid radius, the colloid-swimmer mobility ratio, and the mean number density of swimmers. We also propose a semi-analytical model for the colloid diffusivity in terms of the variance and correlation time of the fluctuating active force resulting from swimmer collisions. In addition, we also analyze interactions between pairs of colloids suspended in an active bath, where our simulations confirm the existence of an effective attractive force, which is the active analog of the depletion force well-known in passive systems. We study the dependence of this active depletion force in terms of the system parameters and explore its role in driving emergent collective dynamics in systems of multiple colloids as recently reported in various experiments. |
Sunday, November 20, 2022 5:53PM - 6:06PM |
J04.00007: A coarse-grained model for cytoplasmic streaming Brato Chakrabarti, Michael J Shelley Cytoplasmic streaming is a striking example of fluid-structure interactions within living cells. Egg cells are among the largest and transporting by diffusion of the proteins necessary for their development is extremely slow. In the later stages of the developing fruit fly egg, a coherent circulatory flow emerges that spans the entire ~200 μm scale cell. This streaming flow is driven by the motion of nanometric motors transporting subcellular cargo along stiff biopolymers (microtubules) anchored at the cell wall. Streaming is crucial for the organism's development, but exactly what functions are fulfilled remain unclear. Here we theoretically investigate the transition to streaming and the consequent transport and mixing. For this, we use a coarse-grained continuum theory that captures the collective response of microtubules and motors that drive the internal flows. This model has the form of a boundary force field fully coupled to an internal Stokesian flow. In particular, we study how flow line topology is influenced by microtubule density and the geometry of the egg cell, as well as first-passage times from sources to sinks. |
Sunday, November 20, 2022 6:06PM - 6:19PM |
J04.00008: Enhanced Transport Barriers with Swimming Microorganisms in Chaotic Flows Ranjiangshang Ran, Paulo E Arratia How does the swimming motion of microorganisms affect the transport and mixing of a passive scalar in complex flows? The answers to this question can potentially improve our understanding of the spread of pollutants (e.g., algal blooms, oil spills) in oceans and lakes, as well as stimulate the development of industrial applications (e.g., biofuel and vaccine productions). In our experiments, we investigate the chaotic mixing of a passive scalar (dye) in dilute suspensions of swimming Escherichia coli. Results show the interaction between the swimming microbes and the dynamical structures of the flow (i.e., Lagrangian coherent structures) can lead to enhanced transport barriers across which the fluxes of the passive scalar are reduced. Discreet particle simulations show that the Lagrangian transport barriers trap passive particles, but repel active particles and cause depletion zones. Overall, our results show that the coupling between activity and Lagrangian coherent structures has nontrivial effects on transport and mixing. |
Sunday, November 20, 2022 6:19PM - 6:32PM Author not Attending |
J04.00009: Programming boundary deformation patterns in active networks Zijie Qu, Jialong Jiang, Heun Jin Lee, Rob Phillips, Shahriar Shadkhoo, Matt Thomson Active materials take advantage of their internal sources of energy to self-organize in an automated manner. This feature provides a novel opportunity to design micron-scale machines with minimal required control. However, self-organization goes hand in hand with predetermined dynamics that are hardly susceptible to environmental perturbations. Therefore utilizing this feature of active systems requires harnessing and directing the macroscopic dynamics to achieve specific functions; which in turn necessitates understanding the underlying mechanisms of active forces. Here we devise an optical control protocol to engineer the dynamics of active networks composed of microtubules and light-activatable motor proteins. The protocol enables carving activated networks of different shapes, and isolating them from the embedding solution. Studying a large set of shapes, we observe that the active networks contract in a shape-preserving manner that persists over the course of contraction. We formulate a coarse-grained theory and demonstrate that self-similarity of contraction is associated with viscous-like active stresses. These findings help us program the dynamics of the network through manipulating the light intensity in space and time, and maneuver the network into bending in specific directions, as well as temporally alternating directions. Our work improves understanding the active dynamics in contractile networks, and paves a new path towards engineering the dynamics of a large class of active materials. |
Sunday, November 20, 2022 6:32PM - 6:45PM |
J04.00010: A few can sometimes move a lot Ebrahim M Kolahdouz, David Stein, Stanislav Y Shvartsman, Michael J Shelley In the realm of embryology and developmental dynamics, there are many circumstances at cellular and sub-cellular levels in which a viscous cytoplasmic flow is stirred or moved by the action of the cytoskeletal assembly. Such activity driven transport can mitigate the ineffectiveness of diffusion-based transport in the crowded cell environment, and in the case of larger cells, yield large-scale net bulk flow. The viscous drag caused by translocating motors and payloads enhances the circulation of the cytoplasm as has been previously observed in the cytoplasmic streaming inside the Drosophila oocyte. In this talk, we study a different streaming mechanism facilitated by the microtubule-dynein assembly within cytoplasmic bridges that connect nurse cells to the oocyte during Drosophila oogenesis. We propose a simple but illuminating model that focuses on how the presence of only a few microtubules in a confined space can rapidly induce and pump a large amount of bulk cytoplasmic flow. We mathematically study the model’s pumping performance and pose the arrangement of microtubules as an optimization problem. We find arrangements that maximize the pumping performance under no constraint on the energy consumption, as well as for a fixed rate of energy dissipation and power consumption of molecular motors. |
Sunday, November 20, 2022 6:45PM - 6:58PM |
J04.00011: Effect of externally imposed shear flow on an active gel in a straight channel Wan Luo, Aparna Baskaran, Robert A Pelcovits, Thomas R Powers Using a minimal hydrodynamic model, we theoretically and computationally study active fluids in a two-dimensional straight channel with the bottom wall translating at a fixed velocity along the channel direction. Using the finite element method, we calculate the critical activity for the fluids to be unstable to spontaneous shear flows and observe that the externally imposed shear flow can stabilize extensile fluids. Additionally, there are three kinds of spontaneous flow states found for extensile fluids: unidirectional flows, translating flows and dancing flows. We characterize these states by the average flow rate and the shear stress imposed by the active flow on the moving wall. Interestingly, we find that contractile fluids can also create a macroscopic spontaneous unidirectional flow when the absolute value of the activity is large enough and the externally imposed shear rate is greater than the liquid crystal relaxation rate. |
Sunday, November 20, 2022 6:58PM - 7:11PM |
J04.00012: Activity induced asymmetric dispersion in confined channels with constriction Armin Maleki, Malihe Ghodrat, Ignacio Pagonabarraga The behavior of particles passing narrow regions and/or constrictions has always been of special interest in traditional microfluidics. The situation becomes far more complex when the moving individuals are living bodies or artificial active particles. In a planar Poiseuille flow, the interplay of self-propulsion and the torque induced by the fluid flow (Jeffrey equation) leads to swinging and tumbling motion of micro-swimmers in the channel [1]. Using Brownian dynamics simulation, we have shown that the patterns of such motions in phase space are modified by imposing a funnel-like constriction in the channel, giving rise to an accumulation of the swimmers on one side of the constriction. Such symmetry breaking in density along the constricted channel, which is also reported in recent experiments [2], goes back to the appearance of attractors in phase space which traps the micro-swimmers in front of the constriction. Our results also indicate that the aspect ratio of elongated micro-swimmers, the ratio of fluid velocity to self-propulsion speed, and the channel confinement are relevant controlling parameters in this phenomenon. |
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