Session T04: Biological Fluid Dynamics: Collective Behavior and Microswimmers III

Noise-induced drift of stochastic swimmers in a Kolmogorov-like flow

We study a model of an elongated, noisy swimmer in a planar Kolmogorov-like flow and investigate the connection between the stochastic swimmer trajectories and the swimmer density in phase space.  Monte Carlo simulations of our model exhibit nonuniform swimmer density profiles in the cross-stream direction, similar to those observed in channel flows.  They also exhibit a highly nonuniform density in the swimmer position-orientation phase space, whose peaks are not easily associated with the phase space structures of the deterministic model.  We propose a new deterministic model for the motion of noisy swimmers which includes a noise-induced drift term added to the swimmer equations of motion.  Our noise drift model possesses attracting limit cycles.  We show that these limit cycles help explain the nonuniform densities we see in the Monte Carlo simulations, and we classify these nonuniform distributions quantitatively using the depletion index.   

Not Participating

Viscosity gradients encountered in the marine ecosystem and gastrointestinal tract can affect the swimming and aggregation of microorganisms. Previous theoretical and numerical studies investigating this phenomenon have considered the effects of spatially differentiated viscous drag and/or propulsion, usually in isolation and using models of swimming with very simplified geometries. However, real active particles combine both effects, often with complex geometries, such as bacteria that swim by rotating flagella. The relative importance of drag- and propulsion-based effects for such active propulsion and the net effect of viscosity gradients on motility is currently unknown. To address these issues, we implement a regular perturbation scheme to numerically investigate the effect of slow varying viscosity fields on self-propelled swimmers with varying geometries and compare how viscosity gradients affect both drag and propulsion.   

Sedimentation of active fluids: Bacteria hinders passive particle sedimentation rates

Numerous natural systems showcase the sedimentation of particles in presence of microorganisms. Here, we experimentally investigate the effects of bacteria activity on the sedimentation process of dilute suspensions of (passive) particles. Presence of swimming bacteria (E. coli) significantly reduces the speed of the sedimentation front of Brownian passive particles; but passive particles did not seem to affect the sedimentation rates of bacteria. Two fronts appear during the sedimentation process, a spherical particle front and a bacteria front. The develop an active hindering settling function which shows the typical decrease in particle sedimentation as bacteria volume fraction increases, followed by a regime in which particle sedimentation speed is independent of bacterial volume fraction.  Results show that a timescale of the second front (E. coli) captures the behavior of both regimes and sedimentation rates of spherical colloids can be tuned via a-priori quantification of bacteria-particle interactions.   

A Flow-Physics-Informed Dynamic Model of Collective Swimming in Fish

            The collective movement of fish in schools is driven not just by behavioral imperatives (such as safety from predators, improved foraging, etc.) and propulsive forces, but also by the hydrodynamic forces induced by the complex flow field encountered by fish swimming in a school. Hydrodynamics also plays a key role in enabling a fish to sense the position/velocity of neighbors and to control its own velocity and heading. Finally, hydrodynamic interactions can be exploited by fish in schools to improve swimming performance. A model of collective swimming that allows the investigation of behavior, as well as hydrodynamic sensing and energetics, could help answer questions related to the behavioral ecology of fish as well as the design of bioinspired swimming systems. In the current study, we present a new model of collective swimming of fish that has three key features: (a) the model is based on the balance of forces and moments on the fish; (b) the model includes interaction with the vortex wakes of fish; (c) the model is parametrized via data from direct numerical simulations (DNS) of a swimming fish. The complex collective swimming patterns that emerge from this model are analyzed and recapitulated against observations. The implications of model predictions for hydrodynamic sensing, control, and hydrodynamic efficiency are also explored.   

Hanging by many tails: Collective underwater breathing in entangled aquatic worms

Many aquatic organisms leverage hydrophobic and hydrophilic body structures to live above and below the water surface. In this talk, we will discuss how California blackworms (Lumbriculus variegatus) use their tails to collectively breath underwater. Typically, these worms burrow and anchor their heads into granular substrates while simultaneously lifting their tails up vertically. The tail, which is used for gas exchange, forms a right angle as it reaches the air-water interface. Due to its material nature, these tails break water surface tension, allowing a worm to “latch” and hang freely onto the surface. In the absence of substrates, individuals instead form a physically entangled “blob” and utilizes this emergent structure as an anchor. We discover that as more blackworms latch onto the surface and entangle together, they can collectively lift off the ground and float, essentially creating a “worm buoy”. We hypothesize that this conformation allows smaller worms to reach the surface for respiration. Additionally, we discover a complex system of alternating hydrophobic segments and hydrophilic intersegments on the tails that facilitate this interfacial latching and unlatching, which we validate with simple physical models and force measurements.   

Collective behavior of platelets defines macroscale properties of blood clots

Blood clots are an active biological material in which platelets extend micrometer-long filopodia to impose contractile forces on the fibrin scaffold that lead to drastic macroscopic changes in clot volume and elastic modulus. Blood clots are involved in physiologic and pathologic processes, and blood clotting disorders prevent the body's natural ability to achieve hemostasis and lead to bleeding, stroke or heart attack. Understanding the underlying physics behind the clotting process is essential to developing treatment of these disorders. We develop and experimentally validate a mesoscale computational model to examine the biophysics of clot contraction by directly linking the microscale platelet movements to macroscale blood clot properties and behaviors. We examine how the collective work of platelets contracting surrounding fibrin network determines the clot forces and structure. Furthermore, we probe red blood cell retention during the blood clotting process. Our work provides insights for developing synthetic and hybrid active composite materials with adaptive mechanical property and behavior.     

Not Participating

The bacterial dynamics and the formation of the deposit at the contact line of an evaporating sessile drop containing Escherichia coli bacteria are studied experimentally. Due to the evaporation, a radially outward flow arises inside the drop which causes an increase in cell density near the contact line. This increase gives rise to the collective motion of cells, which form spatially periodic, radially inward jets. The size of these jets have scales larger than the size of an individual bacteria. We investigate how the wavelength and amplitude of the jets depend on the bacterial motility, density and evaporation rate of the droplet and how the instability evolves over time.   

Dynamics of compressible active nematic fluids

Active nematics are bioinspired fluids with nematic ordering that exhibit chaotic dynamics and self-mixing.  We study a canonical example consisting of a two-dimensional (2D) layer of microtubule bundles and kinesin molecular motors driven by ATP.  Previous work showed that density variations in this system exhibit fractal structure due to the chaotic stretching and folding dynamics, but only when the system is compressible.  Most theoretical models in current use, however, assume incompressibility.  Here, we propose a new set of 2D nematohydrodynamic equations that incorporate compressibility and density variations.  We show how these equations reproduce the fractal density variations discovered in the earlier study, thereby capturing an essential feature of this material in a realistic model.   

Bacteria hinder large-scale transport & mixing in time-periodic flows

Understanding mixing and transport of passive scalars in active fluids is important to many natural (e.g. algal blooms) and industrial (e.g. biofuel, vaccine production) processes. In this talk, we study the mixing of a passive scalar (dye) in dilute suspensions of swimming Escherichia coli in experiments using a two-dimensional (2D) time-periodic flow. Results show that the presence of bacteria hinders large scale transport and reduce overall mixing rate. Stretching fields, calculated from experimentally measured velocity fields, show that bacterial activity attenuates fluid stretching and lowers flow chaoticity. Simulations suggest that this attenuation may be attributed to a transient accumulation of bacteria along regions of high stretching. Spatial power spectra and correlation functions of dye concentration fields show that the transport of scalar variance across scales is also hindered by bacterial activity, resulting in an increase in average size and lifetime of structures. On the other hand, at small scales, activity seems to enhance local mixing; the probability distribution of the spatial concentration gradients is nearly symmetric with a vanishing skewness. Overall, our results show that the nonlinear coupling between activity and flow can lead to nontrivial effects on mixing and transport.   

Bifurcations in suspensions of confined biased microswimmers

We study the emergence of collective dynamics in a suspension of confined Stokesian swimmers whose orientation is set by external cues. With an initially symmetric system, we show that increasing the strength of the alignment as well as the suspension density leads to a successive bifurcations, first to unsteady flows and eventually to symmetry-breaking at the level of the entire suspension. We study the system numerically, elucidate analytically the physical mechanism responsible for the instability, and relate our results to recent experimental findings.    

Not Participating

Chemotaxis is the phenomenon by which active swimmers migrate towards regions of higher chemical concentration, a feature that is crucial to their survival. Swimmers such as E. coli are capable of generating their own attractant which gives rise to self-signaling among active swimmers in a suspension. Experiments (Budrene & Berg 1991, 1995) and theories (Brenner et al. 44 (1998), Keller & Segel (1970)) involving auto-chemotactic suspensions of swimmers have shown the creation of instabilities in these systems, resulting in a clustering of these swimmers. This work explores the role of active-stress driven fluid motion, arising from the motility of the swimmers, on the creation of instabilities in auto-chemotactic suspensions of pushers and pullers.   

Not Participating

Similarly to their biological counterparts, suspensions of chemically active autophoretic swimmers exhibit nontrivial dynamics involving self-organization processes as a result of inter-particle interactions. Using a kinetic model for dilute suspensions of autochemotactic Janus particles, we analyse the effect of a confined pressure-driven flow on these collective behaviors and the impact of chemotactic aggregation on the effective viscosity of the active fluid. Four dynamic regimes are identified when increasing the strength of the imposed pressure-driven flow, each associated with a different collective behaviour resulting from the competition of flow- and chemically-induced reorientation of the swimmers together with the constraints of confinement. Interestingly, we observe that the effect of the pusher (resp. puller) hydrodynamic signature, which is known to reduce (resp. increase) the effective viscosity of a sheared suspension, is inverted upon the emergence of autochemotactic aggregation. Our results provide new insights on the role of collective dynamics in complex environments, which are relevant to synthetic as well as biological systems.