Session E06: Biological Fluid Dynamics: Collective Behavior and Microswimmers (3:10pm - 3:55pm CST)

Life in a Tight Spot: How Bacteria Swim in Heterogeneous Media

Diverse processes in healthcare, agriculture, and the environment rely on bacterial motility in porous media; indeed, most bacterial habitats---e.g., biological gels, tissues, soils, and sediments---are heterogeneous porous media. However, while bacterial motility is well-studied in homogeneous environments, how confinement in a porous environment impacts bacterial transport remains poorly understood. To address this gap in knowledge, we combine microscopy, materials fabrication, and microbiology to investigate how \textit{E. coli} moves in 3D porous media. By probing single cells, we demonstrate that the paradigm of run-and-tumble motility is dramatically altered by pore-scale confinement. Instead, we find a new mode of motility in which cells are intermittently and transiently trapped as they navigate the pore space; analysis of these dynamics enables prediction of bacterial transport over large length and time scales. Further, by developing a new 3D printing approach, we design multi-cellular communities with precise control over the spatial distribution of bacteria. Using this approach, we show that concentrated populations can collectively migrate through a porous medium---despite being strongly confined---and develop principles to predict and direct this behavior.   

Bacterial motion and spread in porous media

We will present a continuum model that describes the collective dynamics of micro-swimmers such as bacteria through a porous wet material. The motion of the swimmer suspension is coupled to the fluid dynamics that is modeled through a Stokes-Brinkman equation with an added active stress. The linear stability of the uniform isotropic state reveals that the suspension transitions from a long-wave instability to a mid-range one where the collective bacterial chaotic motion is weakened. Simulations of the full nonlinear system confirm the analytical results. We discuss the spread of an initial accumulation of bacteria and show the speed of the resulting waves depends non-trivially on the medium porosity. Lastly, we will discuss the dynamics of a bacterial suspension through a structured surface.   

Relating surface properties and collective behaviour of auto-phoretic colloids

Janus phoretic swimmers (JPs) spontaneously exhibit nontrivial collective dynamics within suspensions. Such dynamics arise from (i) the self-propulsion velocity of the particles, (ii) the attractive/repulsive chemically-mediated interactions between particles and (iii) the flow disturbance they introduce in the surrounding medium. These ingredients are determined by the shape and physico-chemical properties of the colloids' surface. Owing to such link, we derive a kinetic model$^{\mathrm{1}}$ for dilute suspensions of chemically-active JPs where the particles' far-field hydrodynamic and chemical signatures are intrinsically linked. Using linear stability analysis of a dilute suspension, we show that self-propulsion induces a wave-selective mechanism for certain particles' configurations consistent with experimental observations$^{\mathrm{2}}$. Numerical simulations of the complete kinetic model are performed to analyse the relative importance of chemical and hydrodynamic interactions in the nonlinear dynamics. Our results show that regular patterns in the particle density are promoted by chemical signalling but prevented by the fluid flows generated collectively by the polarized particles for both puller and pusher swimmers.   

It's dispersion, not diffusion: An exact transport equation for active swimmer suspension from the Smoluchowski equation.

A dilute suspension of micro-swimmers can be modelled with the Smoluchowski (a.k.a. Fokker-Planck) equation for the probability density function of swimmers' location and orientation. However, in most applications, we are only concerned with the locational distribution of swimmers, while the direct numerical simulation of both the orientation and location of swimmers is too computational costly. Therefore, there have been several models to coarse-grain the Smoluckowski equation into a transport equation for the swimmer density. The generalised Taylor dispersion theory (GTDT) has, by far, been shown to be the superior model among others, but its application is strictly limited to pure shear flow. In this presentation, we will present a novel way to derive a transport equation via a transformation of the Smoluchowski equation. The resulting model is less restrictive and exact, which also implies that it is more accurate than GTDT. We will use the gyrotactic swimmer as an example to show that the imposition of positive-definiteness to the diffusivity tensor causes the GTDT model to lose accuracy. The result demonstrates that the biased random walk of swimmers is better described as dispersion rather than diffusion.   

Exact phoretic interaction of two chemically active particles

We study the nonequilibrium interaction of two isotropic chemically active particles taking into account the exact near-field chemical interactions as well as hydrodynamic interactions. We identify regions in the parameter space wherein the dynamical system describing the two particles can have a fixed point; a phenomenon that cannot be captured under the far-field approximation. We find that, due to near-field effects, the particles may reach a stable equilibrium at a nonzero gap size or make a complex that can dissociate in the presence of sufficiently strong noise. We explicitly show that the near-field effects originate from a self-generated neighbor-reflected chemical gradient, similar to interactions of a self-propelling phoretic particle and a flat substrate.   

Not Participating

The quest on how to navigate or steer to optimally reach a target is of paramount importance e.g. for airplanes to save fuel while facing complex wind patterns on their way toward a remote destination. Here, we show that the self-generated flow field induced by microswimmers in a low-Reynolds-number solvent can have a strong influence on the required navigation strategy to reach a target fastest. Accordingly, microswimmers follow swimming trajectories that are qualitatively different from those of dry active particles or motile macroagents. In particular, we demonstrate that the resulting optimal microswimming strategy is useful in the presence of fluctuations where it allows reaching a target up to 50% faster than when following the steering strategy which is optimal for its dry counterparts. Our results provide generic insights regarding the role of hydrodynamics and fluctuations on optimal navigation and might inspire future machine-learning based approaches on optimal microswimming.   

Optimal target localization in turbulent environment with olfaction and team search

Locating an odor source is a vital nontrivial task for animals. Turbulent air breaks odor patches into sparse bunches making traditional search strategies ineffective. Male moths have developed, at the individual level, `smart strategies' to find their mates using sparse odor and wind detection. Here, we investigate if a group of cooperating agents can boost performance of a search process. In our model of swarm of agents, an agent navigates in a turbulent environment using its own perceived private information such as odor and wind detections and public information about the decisions made by its peers. We show that, there is an optimal way to blend the two for a group to find an odor source by following almost the direct path to the target. Conversely, groups who discard public information or don't put enough weight on private information are much slower. Our results could prove useful in robotics [Piro et al. PRE 102 (1), 012402 (2020)].   

Chirality-induced bacterial rheotaxis in bulk shear flows

Interaction of swimming bacteria with flows controls their ability to explore complex environments, crucial to many societal and environmental challenges and relevant for microfluidic applications such as cell sorting. Combining experimental, numerical, and theoretical analysis, we present a comprehensive study of the transport of motile bacteria in shear flows. Experimentally, we obtain with high accuracy and, for a large range of flow rates, the spatially resolved velocity and orientation distributions. They are in excellent agreement with the simulations of a kinematic model accounting for stochastic and microhydrodynamic properties and, in particular, the flagella chirality. Theoretical analysis reveals the scaling laws behind the average rheotactic velocity at moderate shear rates using a chirality parameter and explains the reorientation dynamics leading to saturation at large shear rates from the marginal stability of a fixed point. Our findings constitute a full understanding of the physical mechanisms and relevant parameters of bacteria bulk rheotaxis.   

Low-$Re$ swimming across viscosity gradients, II: Theory

To understand the experiments presented in "Low-$Re$ swimming across viscosity gradients, I: Experiments", we develop a hydrodynamic model to describe the motion of a helical swimmer across a viscosity gradient formed by two miscible fluids. We assume that the resistive force theory of slender filaments is locally valid on the helical propeller and we calculate the swimming speed as a function of the position of the swimmer, relative to the fluid-fluid interface. Comparing with macro-scale experiments, our model accurately predicts the motion of the swimmer when it crosses from low to high viscosity. When crossing in the opposite direction, gravitational forces become important and we modify our model to include buoyancy. In general we find that it is harder for a pusher swimmer to cross from low to high viscosity, whereas for a puller swimmer it is the opposite. Our model is also extended to the case of a continuous viscosity gradient.   

Mechanical pressure of bacterial suspensions

Mechanical pressure exerted by swimming microswimmers show unique properties different from its counterpart in thermal equilibrium systems. Although the mechanical pressure plays a central role in various theories of active fluids, systematic experimental study of the pressure is still few and far between. Here, we investigate the mechanical pressure of suspensions of Escherichia coli (\textit{E. coli}) in quasi-two-dimensional systems of different boundaries. For fixed boundaries, the pressure shows a non-trivial dependence on the geometry of the boundaries, suggesting the non-thermodynamic nature of the mechanical pressure. We further explore the interaction between \textit{E. coli} and freely-moving semi-flexible walls composed of DNA-linked colloidal chains. The chains show enhanced diffusion in bacterial bath, where the diffusivity decreases with the increase of chain length. We construct a simple model based on the hydrodynamic alignment of \textit{E. coli} with the walls, which quantitatively explain experimental findings. Our results shed light on the complex interplays between hydrodynamic interactions, boundary geometries, and mechanical pressures of active bacterial suspensions.   

Low-$Re$ swimming across viscosity gradients, I: Experiments

The environment of many microorganisms consists of fluids with non-homogeneous viscosity distribution, in particular in a biological setting. Some swimmers are able to modify their motion in response to changes in the viscosity, and thus to display so-called viscotaxis. A particular example of a viscotactic bacterium is \textit{H. pylori}, which is able to swim across the mucus layer that protects the stomach and successfully colonise it. In this work we use a synthetic swimmer to study the process in a controlled manner. A magnetically driven helical swimmer is made to swim across a two-layer fluid with contrasting viscosities. The speed of the swimmer, which maintains the same rotational speed, is measured during the penetration process. Tests were conducted for swimmers with the head-first (pushers) and tail-first (pullers), and in the direction of the viscosity gradient and against it. The results reveal widely dynamics, depending on these factors. In general, pushers experience a decrease in swimmer speed during the crossing while pullers experience the opposite effect.   

A geometric constraint minimization algorithm for concentrated active suspension

We present a direct particle-simulation algorithm for concentrated active suspensions composed of slender, self-propelling Brownian rods. The rod motion and rod-rod hydrodynamic interactions are described using a slender-body model proposed by Saintillan and Shelley ["Emergence of coherent structures and large-scale flows in motile suspensions," J. R. Soc. Interface, 9:571, 2012]. Moreover, we implement a geometric constraint minimization technique to avoid particle penetration when rods are subjected to frequent collisions. We perform simulations in the periodic cubic domain across volume fractions, with the maximum volume fraction up to about 40\%. In semi-dilute cases, we demonstrate the algorithm can successfully capture critical behaviors such as the transition to large-scale collective dynamics as predicted by mean-field theories. Moreover, in the concentrated regime, we can track density fluctuations, coherent flows, as well as the evolution of topological structures due to the nematic alignment of motile rods.   

Density fluctuations and collective motions of three-dimensional bacterial suspensions

Active fluids such as bacterial suspensions exhibit unusual large density fluctuations, the so-called giant number fluctuations, defying the conventional wisdom on the density fluctuations of equilibrium systems. While theoretical studies have predicted a non-trivial dependence of density fluctuations on the dimensionality of systems, the fluctuations have only been examined experimentally in two-dimensional (2D) active systems hitherto. Here, we study the density fluctuations of three-dimensional (3D) bacterial suspensions and image the emergence of the giant number fluctuations as the bulk suspensions develop collective motions. Particularly, we observe a gradual increase of density fluctuations with bacterial concentrations, where the rise of giant number fluctuations precedes the formation of the collective motions. At high bacterial concentrations, the density fluctuations observed in our 3D system are significantly stronger than those in 2D systems in existing experiments, contradicting the theoretical predictions. Furthermore, using a genetically engineered light-controlled bacterial strain, we investigate the temporal evolution of density fluctuations through the transition into collective motions and explore the relation between density fluctuations and flow fields. A coupling between the flow divergence and the spatiotemporal variation of density is found, revealing the microscopic origin of the giant number fluctuations. Our experiments provide new insights into the density fluctuations in 3D active fluids and enrich the understanding of the collective dynamics of microbiological systems.   

Collective behavior of heterogeneous platelets during blood clotting.

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. Interaction between platelet and fibrin network leading to blood clot contraction is a complex multiscale process taking place in blood flow. We develop and experimentally validate a mesoscale computational model to examine the biophysics of clot contraction. The model considers platelets actively contracting polymerized fibrin mesh. The model correctly predicts bulk clot volume contraction and kinetics. The model shows that the heterogeneities involved in platelet contraction behavior enhance both clot volume contraction and clot force. We use the model to examine how fibrin network properties affects blood clotting and forces generated by the clot.   

Coarsening in the 2D Incompressible Toner-Tu Equation: Signatures of Turbulence

We investigate coarsening dynamics in the two-dimensional (2D), incompressible Toner-Tu equation. We show that coarsening proceeds via vortex merger events, and the dynamics crucially depend on the Reynolds number ($\mathrm{Re}$). For low $\mathrm{Re}$, the coarsening process has similarities with Ginzburg-Landau dynamics. On the other hand, for high $\mathrm{Re}$, coarsening shows signatures of turbulence. In particular, we show the presence of an enstrophy cascade from the inter-vortex separation scale to the dissipation scale.   

Microswimmers near elastic interfaces

The motion of a swimming microorganism encountered in natural settings is often subject to external cues. These could, for instance, be on account of a complex imposed flow, swimmer-swimmer interactions, or due to presence of boundaries. While a typical scenario consists of a combination of such interactions, of particular interest is the role of confinement. In the latter case, simulations and theories have shown that microswimmers subject to confinement between parallel rigid boundaries exhibit an excess accumulation near the boundaries. In turn, the active pressure forces on the wall increase with increase in confinement. In the present study, we relax the rigidity constraint and consider the interaction of microswimmers with elastic interfaces. In particular, the forces that develop on account of the swimmer-wall interaction are analyzed, for a linearly elastic wall.   

Learning to Cloak Swimming Objects in Viscous Environments using a Flock of Artificially Intelligent micro-Robots

Here, we present a systematic methodology to actively cloak swimming objects within any arbitrarily crowded suspension of micro-swimmers. Our approach is to conceal the target swimmer throughout its motion using an interacting flock of swimming agents equipped with adaptive decision-making intelligence. Through a reinforcement learning algorithm, the cloaking agents experientially learn optimal behavioral policy in the presence of flow-mediated interactions. This artificial intelligence enables them to dynamically adjust their swimming actions, so as to optimally form and robustly retain any desired arrangement around the moving object without disturbing it from its original path. Therefore, the presented active cloaking approach is both robust against disturbances and non-invasive to the motion of cloaked objects. We then demonstrate how the trained cloaking agents can be readily used, in any region of interest, to realize hydrodynamic invisibility cloaks around any number of arbitrary intruders. Our findings provide a clear road-map toward realizing hydrodynamic invisibility cloaks for externally or internally controlled artificial swimming micro-robots, which paves the path toward non-invasive intrusion of swimming micro-robots with a broad range of biomedical applications.   

Shape matters: A Brownian microswimmer in a channel

We consider the active Brownian particle model for a two-dimensional microswimmer with fixed speed, whose direction of swimming changes according to a Brownian process. The probability density for the swimmer evolves according to a Fokker--Planck equation defined on the configuration space, whose structure depends on the swimmer's shape, center of rotation, and domain of swimming. We enforce zero probability flux at the boundaries of configuration space. We derive a reduced equation for a swimmer in an infinite channel, in the limit of small rotational diffusivity, and find that the invariant density depends strongly on the swimmer's precise shape and center of rotation. We also give a formula for the mean reversal time (MRT) : the expected time taken for a swimmer to completely reverse direction in the channel. Using homogenization theory, we find an expression for the effective longitudinal diffusivity of a swimmer in the channel, and show that it is bounded by the MRT \footnote[1]{arXiv:2006.07714 [cond-mat.soft]}. A novelty in our work is to include the center of rotation as a parameter, which changes a swimmer's tendency to align with walls.   

Activity and density dependence of collective states in confined bacterial suspensions

Suspensions of microswimmers such as swimming bacteria, algae and spermatozoa are naturally found in confined spaces. To understand how geometric confinement affects the collective behavior of microswimmers, we conduct experiments using genetically engineered \textit{Escherichia coli}, whose swimming speed can be controlled via the intensity of illuminating light. We find that the \textit{E. coli} suspensions, when placed in quasi-two dimensional Hele-Shaw cells, exhibit various ordered states that are not seen in their three dimensional counterparts. Particularly, by tracking the positions and orientations of individual bacteria, we identify three distinct states, i.e., a disordered state, a laning state with nematic symmetry, and a swarming cluster state with polar alignment. A phase diagram of bacterial suspensions under confinement is mapped as a function of the concentration and swimming speed of bacteria. We also discuss the nature of interactions that are responsible for the emergence of the ordered states. Our study provides an experimental benchmark for understanding the collective behavior of microswimmers in confined geometries, laying emphasis on how emergent ordered states depend on the dimensions and boundaries of the system.   

Low Reynolds number, bi-flagellated Quincke swimmers with multiple forms of motion

In the limit of zero Reynolds number (Re), swimmers propel themselves exploiting a series of non-reciprocal body motions. For an artificial swimmer, a proper selection of the power source is required to drive its motion, in cooperation with its geometric and mechanical properties. Although various external fields (magnetic, acoustic, optic, etc.) have been introduced, electric fields were rarely utilized to actuate such swimmers experimentally in unbounded space. Here we demonstrate the viability to generate locomotion of a bi-flagellated sphere at low Re via Quincke rotation using uniform and static electric fields. These Quincke swimmers exhibit three different forms of motion, including a novel self-oscillatory state due to elasto-electro-hydrodynamic interactions [1]. Each form of motion follows a distinct trajectory in space. Our experiments and numerical results demonstrate a new method to generate, and potentially control, the locomotion of artificial flagellated swimmers. [1] L. Zhu and H. A. Stone, Phys. Rev. Fluids, 4, 061701(R), 2019.   

Fractal generation in self-driven active nematic fluids

Active fluids, composed of individual self-propelled agents, can generate complex large-scale coherent flows. A particularly important and popular laboratory realization of such an active fluid is a system composed of microtubules, aligned in a 2D nematic phase, and driven by ATP-fueled kinesin biomolecular motors. This system exhibits robust chaotic advection, giving rise to a pronounced fractal structure in the nematic contours. Though these fractal patterns are reminiscent of passively advected dye in 2D chaotic flows at low Reynolds number, the underlying mechanism for fractal generation is more subtle in active nematics. In this talk, we present an alternative theory for fractal generation and compare the predicted fractal scaling to experimental data.   

Long-range interactions dominate surface accumulation of Chlamydomonas reinhardtii

Swimming microorganisms accumulate near solid surfaces in their environment. This has implications for the process of surface colonisation. For extensile swimmers, long-range hydrodynamic interactions have been shown to play a role in governing this near-surface accumulation. Such interactions’ role in the accumulation of contractile swimmers is less clear. We investigate the roles of surface scattering and long-range interactions in the near-surface accumulation of a model contractile swimmer. A population of C. reinhardtii swimming within a large volume, bounded by two flat surfaces, was recorded simultaneously by four cameras, and a large sample of 3D cell trajectories triangulated. We derived statistics of the cells’ isotropically diffusive swimming kinematics as well as their surface scattering dynamics, and observe a long-range cell-surface interaction. These statistics were sampled to build an empirically-driven Markov Chain Monte-Carlo simulation. In this way, we directly link the population’s near-surface accumulation to the cells’ swimming, scattering and surface interaction dynamics. We find that the experimentally observed population distribution can only be accounted for by including, in the model, the long-range cell-surface interaction characterised experimentally.   

Pattern stabilisation in programmable active matter

Ordered patterns of drones or robotic agents are useful for many purposes such as surveying unknown territory, taking measurements of scientifically important quantities over a large area. Unlike birds, which naturally organise themselves to counteract destabilisation due to a turbulent environment, stabilising a patterned swarm of drones is energetically expensive and requires extensive computation and communication overheads. We propose an energy-efficient algorithm for creating stable, ordered, swarms of active robotic agents arranged in any given pattern. The strategy involves suppressing a class of fluctuations known as “non-affine” displacements, viz. those involving non-linear deformations of a reference pattern while allowing affine deformations. This is achieved using precisely calculated, fluctuating, thrust forces associated with vanishing average power input. A surprising outcome of our study is that once the shape of the swarm is maintained at a steady-state, the statistics of the underlying flow field is determined solely from that of the a-priori known forces needed to stabilize the swarm. Therefore, such techniques will be useful in studying the turbulent flow where direct measurement of flow velocities is difficult.   

Instabilities driven by diffusio-phoretic flow on catalytic surfaces

The solutal concentration gradient along a surface can induce a diffusio-phoretic flow. Here we theoretically and numerically investigate the instability driven by diffusio-phoretic flow. The important control parameter is the P\'eclet number $Pe$, which quantifies the ratio of the solutal advection rate to the diffusion rate. We first study the diffusio-phoretic flow on a catalytic plane by two-dimensional simulations. We have found that when $Pe > 8\pi$, the mass transport by convection overtakes that by diffusion, and a symmetry-breaking mode arises. When $Pe > 16\pi$, multiple concentration plumes are emitted from the catalytic plane, which eventually merge into a single larger one. When $Pe$ is even larger ($Pe > 603$ for Schmidt number $Sc=1$), there are continuous emissions and merging events of the plumes. Finally, we conduct three-dimensional simulations for spherical catalytic particle, and again find continuous plume emission and plume merging. Our results help understand the chaotic motion of catalytic particles in the high $Pe$ regime.   

Dispersion statistics of microswimmers in turbulence

Many plankton species are motile. Motility is, for example, key for grazing and evading predation. Apart from the swimming speed, shape is a critical parameter in defining the response to hydrodynamic flows. A comprehensive understanding of the relation between the relevant microswimmer parameters, shape and motility, and their transport properties and rotation rates in turbulent flows is still missing. Here, we study self--propelled ellipsoids in turbulence as a simple model for motile microorganisms in aquatic environments. Using direct numerical simulations, we find non--trivial dispersion properties and rotation statistics as a result of a complex interplay between turbulent advection, motility, and particle spinning and tumbling rates. We show that one important aspect is the effect of rotation on particle transport. In contrast to spinning, tumbling constantly changes particle orientation. As tumbling rates are shape--dependent, this leads to intrinsically different transport properties for differently shaped particles. Our investigation thus helps to characterize the intricate dynamics of microswimmers in turbulent flows and sheds light on the role played by shape and motility.   

Topological Mixing in the Vicsek Model of Active Matter

A general feature of active matter systems is that they consume energy on the small scale and coherent flows emerge on the large scale. Whether the units comprising these systems are bacteria, birds, or the microtubules of active nematics, coherence arises due to local interactions. In a now classic model, the Vicsek model, coherence, as measured by an order parameter, undergoes a phase transition with the changing importance of local interactions. We revisit this result from the perspective of mixing and fluid advection. In particular, we use a measure of dynamic disorder, the topological entropy, which captures the complexity of how the trajectories of these active agents wind about one another. We are able to calculate this mixing measure, and probe the thermodynamic limit of larger ensembles of agents, thanks to a new algorithm, which combines ideas from low dimensional topology and computational geometry. We will show some interesting results in how this disorder parameter behaves as we change the importance of local interactions.   

Collective motion and aggregation of active inclusions on biological membranes

We study hydrodynamic aggregation of active membrane inclusions within biological membranes. The typical cell membrane is a crowded assembly of molecular motors and biomolecules embedded in a 2D fluid mosaic. Active molecular motors perform complex cellular tasks by binding, releasing, and changing conformations, inducing hydrodynamic flows in the membrane and the surrounding fluid. These long-ranged hydrodynamic fields perturb neighboring inclusions, leading to large-scale collective dynamics. We illustrate these novel flow physics by theoretically examining a pair of hydrodynamically interacting membrane inclusions. Pairs display unique oscillatory dynamics that disappear when the 3D fluid adjacent to the membrane is confined. The phase behavior of the pair problem reveals the underlying mechanisms and suggests strategies for control of large-scale aggregation. Building on these insights, we perform numerical simulations to show that bulk confinement introduces flows on the membrane that favor aggregation. Traditional engineering of foreign inclusions in membranes has targeted interactions due to capillarity, curvature and electrostatics; we propose hydrodynamic confinement as an additional controllable parameter to tune collective motility and aggregation on lipid membranes.   

Active Particle Based Selective Transport and Release of Cell Organelles and Deformation of a Single Nucleus

Isolation of cell organelles is important as it enables their direct investigation as means for cell analysis. Current organelle separation methods include density-gradient centrifugation...().., immunoisolation and electromigration analysis. We applied a mobile floating microelectrode to trap and transport cell organelles (nucleus, mitochondria and lysosome) in a selective and releasable manner. This selectivity is driven by the different dielectrophoretic (DEP) potential wells on the JP surface that are controlled by the frequency of the electric field, along with the hydrodynamic shearing and size of the trapped organelles. Hence, the active carrier constitutes an important and novel ex vivo platform for manipulation and mechanical probing of subcellular components of potential for single cell analysis.   

Run-to-tumble switching noise controls the residence time of E.coli bacteria at solid surfaces

Using a 3D Lagrangian tracking technique, we monitor wild-type E.coli bacteria undergoing a run and tumble exploration process at surfaces. We determine the distributions of incoming and escape angles as well as the sojourn times distribution which displays a very broad tail. By directly monitoring the flagella bundling/debundling process, we also determine the mean tumbling times at the surface and in the bulk. To reproduce quantitatively all our data, we extend a model previously developed to describe the free swimming statistics of motile wild-type E.coli [N. Figueroa-Morales et al., Physical Review X, 10, 021004, (2020)]. The model is based on the presence of an internal protein concentration fluctuation which is triggering the run to tumble switch. It leads to a behavioral variability characterized by memory in the run-time sequence and a broad distributions of run times. This results suggest that it would be timely to assess precisely the role of such inherent chemotactic noise in other macroscopic transport processes implying motile bacteria.   

Bistability in the collective behavior of confined fish schools

Fish schools are examples of systems whose collective dynamics emerge from individual-level interactions. These systems are often modeled with self-propelled particles in unbounded domains subject to phenomenological behavioral rules based on visual feedback that usually neglect hydrodynamic interactions among the fish. Little is known on how geometric confinement together with flow-mediated interactions affect the collective behavior of fish. Here, we combine vision-based rules with hydrodynamic interactions in a circular domain, and we map out the different collective phases that the group of fish can achieve. We show that (1) a new collective phase emerges where the group follows the tank wall; (2) the collective phases are insensitive to the light intensity; and (3) a new bistable regime emerges in which the school intermittently switches from schooling to milling and vice-versa. We analyze the bistable regime by constructing effective potentials on the coarse-grained translational and rotational order parameters. We find that the bistable regime is sensitive to the school size and the geometric confinement. We conclude by commenting on how these techniques can be extended to study general stochastic collective dynamics.   

Microbial jets in metabolically driven flows

In liquid environments, interactions between microbial activity and hydrodynamic flows can lead to a large variety of behaviors. In this talk, I will show that when grown on a viscous liquid S. cerevisiae (baker's yeast) can behave like "active matter". The collective metabolism drives a fluid flow many times larger than the colony expansion speed, resulting in mechanical stresses and preferential growth which can generate a jetting phenomenon with yeast cells. I will present laboratory experiments, combined with numerical modeling, and discuss how microbial expansions on a liquid interface provide a versatile system to explore the interplay between hydrodynamics, growth and competition.   

Sperm Have Got The Bends

The journey of development begins with sperm swimming through the female reproductive tract en route to the egg. In order to successfully complete this journey sperm must beat a single flagellum, propelling themselves through a wide range of fluids, from liquified semen to viscous cervical mucus. It is well-known that the beating tail is driven by an array of 9 microtubules surrounding a central pair, with interconnecting dynein motors generating shear forces and driving elastic wave propagation. Despite this knowledge, the exact mechanism by which coordination of these motors drives oscillating waves along the flagellum remains unknown; hypothesised mechanisms include curvature control, sliding control, and geometric clutch. \ \newline In this talk we will discuss the mechanisms of flagellar bending, and present a simple model of active curvature that is able to produce many of the various sperm waveforms that are seen experimentally, including those in low and high viscosity fluids and after a cell has `hyperactivated' (a chemical process thought to be key for fertilization). We will show comparisons between these simulated waveforms and sperm that have been experimentally tracked, and discuss methods for fitting simulated mechanistic parameters to these real cells.   

Active nematic defect dynamics influenced by submerged microstructures

Active nematics represent an interesting framework to study energy-driven defects in structured fluids. We study the behavior of an active microtubule/kinesin fluid in which mobile topological defects are continually created and annihilated, braiding around each other to form a chaotic self-mixing fluid. In this work we present a novel effect: the use of virtual boundaries imposed by submerged microstructures as a strategy to control defect flow dynamics. We use micro-fabrication to prepare complex geometries using SU-8 photoresist. The 2D active layer is confined between aqueous and oil layers, in an experimental geometry designed with structures of different depths directly below the active layer. Flow dynamics of the active phase are investigated using fluorescence microscopy. The boundary effect produces similar defect dynamics to those seen for hard boundaries, including stagnation points near boundaries and positional dependence of defect charges.   

Collective dynamics of run-and-turn microswimmers with finite directional memory

Swimming bacteria and motile colloids perform diverse types of random-walks at the individual level. A population of these active particles exhibit complex collective behaviors. While most of previous numerical models on self-organization in such active matter systems have focused on density and motility-induced pattern formation, we report on the effect of finite directional memory on the emerging collective dynamics. Inspired by our recent experimental findings on colloidal random-walkers, we conduct two-dimensional numerical analysis of correlated random walkers in a confined domain with alignment, anti-alignment and repulsion interactions. We elucidate the role of directional memory on controlling how the long-term patterns evolve from locally short-term transient dynamics. More specifically, we show that the run time and degree of directional memory play a crucial role in establishing different stable collective states in a confined system; e.g. a giant single vortex vs. dynamic vortex lattice. Our findings show the potential for dynamic transitioning between states at constant concentration and activity (speed) of active particles by solely tuning the directional memory of individual random walkers.   

Waltzing worms: the dynamics of plant-animal collective vortex structures

Circular milling, a stunning manifestation of collective motion, is found across the natural world, from fish shoals to army ants. It has been observed recently that the plant-animal worm \textit{Symsagittifera roscoffensis} exhibits circular milling behaviour, both in shallow pools at the beach and in Petri dishes in the laboratory. Here we investigate this phenomenon, through experiment and theory, from a fluid dynamical viewpoint, focusing on the effect that an established circular mill has on the surrounding fluid. Unlike systems such as confined bacterial suspensions and collections of molecular motors and filaments that exhibit spontaneous circulatory behaviour, and which are modelled as force dipoles, the front-back symmetry of individual worms precludes a stresslet contribution. Instead, singularities such as source dipoles and Stokes quadrupoles are expected to dominate. A series of models is analyzed to understand the contributions of these singularities to the azimuthal flow fields generated by a mill, in light of the particular boundary conditions that hold for flow in a Petri dish. A model that treats a circular mill as a rigid rotating disc that generates a Stokes flow is shown to capture basic experimental results well, and gives insights into the emergence and stability of multiple mill systems.   

Shepherding bacterial flocks: Controlling active suspensions through orientable agents

Understanding how large numbers of individual active agents, such as flocks, schools, and swarms of organisms, organise their collective motion in response to changes in the local environment remains a prominent open question in active matter. Focusing on bacterial turbulence in dense suspensions of \textit{Bacillus subtilis}, we investigate the ability of a comparatively small number of magnetic agents to influence the transport properties of the active suspension. A range of different aspect ratio magnetic agents, including immobilised spherical particles and rod-like magnetotactic bacteria (\textit{Magnetospirillum magneticum}, AMB-1), are mixed into dense suspensions of \textit{B. subtilis}, where the motion of the flow fields and individual particles are measured by PIV and particle tracking, respectively. Changes in the structure and spatiotemporal fluctuations of the bacterial turbulence are quantified under a variety of magnetic field strengths. We find that the magnetic torque imposed by non-spherical agents imparts significant anisotropy to the active suspension, thereby linking the large-scale collective behavior to the single cell level interactions.   

The odd flows of a colloidal chiral fluid

We report the assembly of a chiral fluid composed of millions of spinning colloidal magnets. By activating the fluid at the single unit level, we observe macroscopic flows with no counterpart in conventional fluids. Odd viscous stresses drive the propagation of unidirectional free-surface waves damped by odd (or Hall) viscosity. Further, the competition between odd stress and cohesive forces results in intermittent bulk flows, blurring the distinction between solid and liquid.   

Dynamics of active droplets of nematic fluid immersed in a viscous fluid

Coarse-grained continuum descriptions of active suspensions (fluids with extra stresses from the activity of suspended particles) have successfully predicted instabilities, pattern formation and complex dynamics observed in some experimental systems. In this work we examine the dynamics of droplets filled with suspended immotile particles that exert active dipolar stresses on the fluid. We show that the effects of surface tension on the linear instability of the active fluid depends on whether the suspended active particles are extensile or contractile. Based on the linear stability of the active droplet, we are able to find parameters that correspond to various nonlinear droplet dynamics such as a washing machine mode, a steady squirmer, a pulsating squirmer, and a meanderer. Simulations of a small system of such active drops give insight into how the activity inside the drops dictates how they communicate with each other in different parameter regimes.   

Swimming in pairs at intermediate Reynolds numbers

We computationally investigate pairwise interactions at intermediate Reynolds numbers (Re) between simple, reciprocal dumbbell swimmers each composed of two unequally sized spheres. For nonzero Re, our reciprocal swimmer swims small-sphere-leading and interestingly, as Re increases, switches its swimming direction to large-sphere-leading. We vary the separation distance, angle, and phase difference between the swimming pair, and we find several regimes of long-time behavior including different steady pair configurations, bi-stable pairs, spontaneous rotation, and divergence. We also discover configurations where the pair behaves completely different from the single swimmer. Averaged flow fields are analyzed to further understand these stable configurations.   

Numerical study of hydrodynamics interactions in a diamond fish school

Fish school, as an archetypal collective phenomenon in nature, has been proven to provide hydrodynamic benefits to swimming. In a fish school, the spatial arrangement is believed to be one of the most important factors influencing hydrodynamic interactions among individuals. However, the hydrodynamic interactions in a dense diamond school have received little attention. In this work, an immersed-boundary-method-based incompressible Navier-Strokes flow solver is employed to quantitatively characterize the propulsive performance and the flow field of each fish in a diamond school. A parametric study is implemented to investigate the effect of spatial arrangement on the hydrodynamic performance of a dense diamond school. Force production and propulsive efficiency of individuals in a school are compared with that of a singular fish to illustrate the effect. Besides, the corresponding flow field analysis has been done to reveal the underlying fluid mechanisms. This enables us to gain more insight into the design of underwater robotic swarms.   

Simulating fluidization of black soldier larvae

Active systems can be driven via the internal activity of individual elements or via external mechanical forcing. Here we study a living system in which both internal and external activity can be varied. In laboratory experiments, we confine thousands of ~10 mm long black soldier fly larvae in an air fluidized bed (~4 larva lengths in diameter, 10 in height ) and study the collective and individual dynamics. When larvae are cooled such that internal activity is suppressed, the system, behaves like a typical fluidized bed: as airflow rate $Q$ increases from zero, the height of the column remains fixed until the pressure drop through this living porous medium balances the weight per area of the larvae. At this point, the height of the column increases with increasing $Q$ while the pressure remains fixed. Active larvae display qualitatively different dynamics such that bed height remains approximately fixed for low $Q$ and begins to increase well before the pressure-balance fluidization transition. Defluidization dynamics (decreasing $Q$) are similar in both active and inactive larvae. We gain insight into these phenomena in coupled computational fluid dynamics and agent-based simulations.   

Separating motile and immotile bacteria through confined chemotaxis

The majority of bacteria move in complex porous materials, such as tissues or soil, yet their motion and chemotaxis in confinement is not yet completely understood. We will present a model that couples individual tun-and-tumble bacterial motion to the chemical gradient while the entire colony is inside a simple circular confinement. We will discuss the states observed for various parameters, and also the phase separation in an initially random mixture of motile and immotile bacteria.   

Bacteria Hinder Large Scale Transport in 2D Time-Periodic Flows

Understanding mixing and transport of passive scalars in the presence of swimming microorganisms is important to many natural (e.g. algal blooms) and industrial (e.g. biofuel) processes. Here, we experimentally study the mixing of a passive impurity in 2D time-periodic flows that is seeded with different concentrations of swimming E. coli. Dye experiments show that bacteria hinder large scale transport and reduce overall mixing rate, which decreases as bacteria concentration increases. Energy spectra analysis reveals that, at early times, bacteria promote small scale structures by injecting energy at smaller wavelengths. At longer times, we find a substantial energy increase at all wavelengths, suggesting bacteria work against energy cascade. Velocimetry shows that bacteria can attenuate vorticity and systematically decrease the Finite-Time Lyapunov Exponent (FTLE) of the system compared to flows without bacteria at same Reynolds numbers. Overall, our results show that large scale transport and mixing are hindered by the presence of bacteria, despite the formation of small-scale structures locally.   

Hindering particle sedimentation in the presence of swimming E. coli

How passive particles sediment in the presence of micro-organisms such as bacteria is a question that remains unanswered. To address this question, we experimentally investigate the effects of bacteria activity on the sedimentation process of dilute suspensions passive particles. Results show that the presence of swimming bacteria (E. coli) significantly reduces the speed of the sedimentation front of a dilute suspension of Brownian particles; in this dilute regime, but passive particles did not seem to affect the sedimentation speed of bacteria. We also find that bacteria increase the dispersion of the settling passive particles, measured by the width of the sedimentation front. Mean square displacement data shows that bacterial activity decays over long experimental (sedimentation) times. An advection-diffusion equation coupled to bacteria population dynamics seems to capture concentration profiles relatively well. A single parameter, the ratio of single particle speed to the bacteria flow speed can be used to predict front sedimentation speed.   

Fluid Elasticity enhances Mammalian Sperm Cells propulsion speed

While much is known about swimming of mammalian sperm cells in Newtonian fluids, there is still much to be learned about the effects of fluid elasticity on the swimming behavior of sperm cells. Here, we discuss results from a systematic experimental investigation of sperm cells swimming in polymeric fluids with different levels of elasticity; results are compared to Newtonian fluids of similar viscosities. We find that in general sperm cells swimming speed decreases as fluids viscosity increases for both viscoelastic~and Newtonian fluids.~However, as the viscosity increases, the decay in swimming speed in polymeric solutions is much less pronounced than in Newtonian solutions; that is, the swimming speed asymptotes~to a larger value for viscoelastic than for Newtonian fluids at high viscosities. We also find that sperm swimming speed increases as fluid elasticity (or Deborah number) increases.~We quantify changes in kinematics and swimming gait and show how they can account for the significant enhancement in sperm motility in non-Newtonian fluids.~Overall, our results show sperm cells can swim faster in viscoelastic than in Newtonian fluids of same viscosity, suggesting that viscoelasticity may enhance sperm swimming speed.   

Spatiotemporal optimal control of active nematics actuated by activity strength and vorticity

Active nematics are an important class of active fluids comprising stress-generating, anisotropic constituents. When the active stress generated is extensile, buckling instabilities create motile topological defects that drive chaotic hydrodynamics. Understanding how to control the fluid flows created by these materials will further our understanding of biological processes and inform design of active, synthetic materials. We demonstrate the use of two different spatiotemporal control fields: applied vorticity and activity strength (considered separately), to shape the dynamics of an extensile active nematic that is confined to a disk. In the absence of control inputs, the system exhibits two attractors, clockwise and counterclockwise circulating states characterized by two co-rotating topological $+\frac{1}{2}$ defects. We identify spatiotemporal inputs that switch the system from one attractor to the other; we also examine phase-shifting perturbations. Control inputs are identified by optimizing a penalty functional with three contributions: total control effort, spatial gradients in the control, and deviations from the desired trajectory.   

Collective self-propulsion in active and passive apolar coloidal mixtures

Collections of interacting active particles, self-propelling or not, show remarkable phenomena including the emergence of dynamic patterns across different length scales, from animal groups to vibrated grains, microtubules, bacteria, and chemical or field-driven colloids. Artificial active particles convert energy from the environment into net propulsion, breaking detailed balance and even action-reaction law in different many particle systems, a clear signatures of their out-of-equilibrium nature. I will analyze the emerging properties in systems composed by passive and active apolar colloids. The colloidal activity induces activated chemophoretic flows which lead to effective attractive interaction even for systems in which isolated active colloids are apolar. These dynamic interactions lead to collective emergent motion and can promote the formation of a rich variety of self-assembled structures. I will discuss how a combination of a passive cargo and apolar active colloid can form to self-propelling hybrid clusters and will show how increasing the size of the attached non-catalytic cargo, the cluster can reverse its direction, thus providing a general description of how activity and propulsion emerge in a catalytic active and passive mixed system.   

Experimental investigation of pair-wise interactions between Chlamydomonas reinhardtii

Collective dynamics arise in suspensions of motile micro-organisms and is relevant to such biological processes as reproduction and biofilm formation. Such collective motion is thought to arise from the mechanical interactions between motile cells. The nature of these interactions has been investigated previously, to determine the relevance of long range hydrodynamic interactions and short range steric interactions to the emergence of collective motion. In this work, we use a unique multi-camera microscopy set-up to track green alga Chlamydomonas reinhardtii in a dilute suspension. The flow cells used in the experiment are approximately two hundred times the size of one cell. This allows the cells to swim freely in all directions. Three dimensional Lagrangian tracking is performed by using projective geometry and supports the reconstruction of the cell trajectories within one cell radius accuracy. We characterize the interactions between two cells coming within close range. The resulting trajectories provide data by which to examine the pair-wise interactions between two swimming cells. These interactions are discussed in terms of the relevant length and time scale and change in swimming direction.