Session Q05: Biological Fluid Dynamics: Collective Behavior and Microswimmers II

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In simple shear flow, we observed red blood cells (RBC) form synchronized rotating "waltzing" pairs in the slit confined geometry.  We modeled the RBC dynamics with fully coupled hydrodynamic interactions (HI) and without inter-particle adhesion.  We found that shear-induced HI between the disc-shaped particles induce the formation of synchronized rotating doublets at low capillary number (Ca), low Reynolds number (Re), and dilute to moderate RBC volume fractions of φ=3 to 10 %.  In addition, the HI between the RBC and the wall boundaries induce migration towards the slit centerline, resulting in crystalline-like order between the doublets.  At sufficiently high Ca, the doublets dissolve into singlets but continue to flow in evenly-spaced layers.  This collective behavior further effect non-monotonic dependence of the suspension intrinsic viscosity on the flow shear rate and the suspension volume fraction.    

Morphological Stability of Chemotactic Fronts

Fronts – propagating interfaces that allow one spatial domain to invade another – are ubiquitous in nature. One of the most fundamental characteristics of a front is its morphological stability: Do shape perturbations decay or grow over time? While this question is well-studied for diverse classes of fronts, the conditions for the stability of chemotactic fronts – in which active agents collectively migrate in response to a self-generated chemical gradient – remain unknown, despite the prevalence of such fronts in biological and active matter. Here, we combine experiments, simulations, and theory to examine the stability of chemotactic fronts formed by migrating populations of E. coli. We identify two distinct modes in which chemotaxis influences the morphology of the population: cells in different locations along a front migrate at different velocities due to spatial variations in (i) the local nutrient gradient and in (ii) the ability of individual cells to sense and respond to the local nutrient gradient. The competition between these two modes regulates the overall stability of the front. Guided by these findings, we suggest that the cells' sensory machinery might have evolved to ensure stable front propagation. Moreover, as sensing of any stimuli is necessarily limited in living and active matter in general, the link between sensing by individuals and the morphological stability of an entire population revealed by our work may operate in other types of directed migration such as durotaxis, electrotaxis, and phototaxis.   

Lagrangian structure, stretching and transport in bacterial turbulence

In active matter systems, dense suspensions of self-propelled agents spontaneously exhibit large-scale, chaotic flow structures.

Descriptions of the dynamics of these systems have predominately focused on characterization of spatiotemporal correlation of the velocity field, but their transport properties and mixing kinematics remain largely unknown. In this work, we use Lagrangian analysis techniques to study the chaotic flow fields generated by "bacterial turbulence'' in dense suspensions of a model bacterium (Bacillus subtilis). High-resolution velocity fields are measured using particle image velocimetry across a range of bacterial swimming speeds, where the computed Lagrangian stretching visualizes the induced stretching and folding, characteristic of mixing. Close inspection of the finite-time Lyapunov exponent (FTLE) field reveals time and swimming speed dependent FTLE statistics reminiscent of intermittent dynamics in classical chaotic dynamical systems. At moderate Péclet numbers, experiments and Langevin simulations reveal that manifolds of the FTLE field guide scalar mixing and regulate transport in these active suspensions, which is ecologically relevant to the dispersal of chemical resources and particulates in dense bacterial colonies.   

Surveillant and hydrodynamic benefits of fish schooling

This research explores the surveillance capability and hydrodynamic benefits of fish school. It has been argued that fish schooling serves multiple objectives such a finding better resources, enhance swimming performance and protecting against predators attack the group.  In this abstract, we explore the connection between the morphologies of fish schools and the long-range predator detection in species such as allis shad. The radiation and diffraction of sonic and ultrasound waves in different school shapes and sizes are quantified and correlated to the hydrodynamic performance of the school. The model consists of a fish school that shows a typical chess-like formation with a specified spacing between fishes, which is typical for most species. Each fish is represented by a NACA0012 airfoil and the Kutta condition is applied to create the vortex wake behind each fish. The wave propagation is modeled with the boundary integral approach. We will talk about optimal fish length and the separation distance between members of a group to create a supper biological organism that can amplify the low amplitude signal for better detection while benefiting from hydrodynamic interactions between the members.     

To cross or not to cross: the collective swimming of bacteria in two-dimensional confinement

The natural habitats of microorganisms often involve confined geometries, which alter their swimming behavior and mutual interactions. To explore the effect of confinement on the collective behavior of bacteria, we image a suspension of swimming E. coli in a Hele-Shaw cell using bright-field microscopy. By slightly varying the thickness of our cell, we create two closely related confined geometries: a 2D cell where bacteria are strictly confined to a monolayer and unable to cross over each other, and a quasi-2D cell where they can cross over each other out of the plane. We find that the emergent collective behaviors of bacteria are qualitatively different depending on the geometry of the cell. For the quasi-2D geometry, we observe the nematic alignment of bacteria with long-range orientational order. However, for the 2D geometry, the long-range nematic order is replaced by short-range polar order with transient clusters of co-moving bacteria. We show that individual swimming bacterium experiences stronger velocity fluctuations in the 2D geometry, which interrupt the growth of bacterial clusters. Our experiments reveal how a subtle change in the geometric confinement strongly affects the collective swimming of bacteria.   

Schooling Behavior of Antarctic Krill Under Various Flow and Light Conditions

Antarctic krill (Euphausia superba) are an ecologically important species in the Southern Ocean food chain and swim in schools that extend several kilometers horizontally and hundreds of meters vertically. Krill schools are thought to increase swimming efficiency and enhance their collective response to environmental cues such as flow, light, and the presence of predators and prey. However, little is known about how krill schools respond to these cues. We built a novel annular flume having inner and outer diameters of 0.3 m and 1.2 m, respectively, a water depth of up to 0.3 m, and the capability of generating flows on the order of 1-100 mm s^-1. Flow was generated by rotating the inner cylinder and by submersible pumps and flow conditioners positioned along the outer wall and was characterized using particle image velocimetry (PIV). We conducted experiments at Palmer Station, Antarctica, where 700 krill were placed in the tank at a density of 5 krill L^-1 and were subjected to flow speeds of approximately 15 and 30 mm s^-1 at two different light levels. We filmed krill schools with a stereophotogrammetry system at 23.7 fps, and analyzed 3.5 minutes of footage per trial. Deep learning software and computer algorithms were used to measure krill positions in 3D space and time. Swimming speeds, school polarity, nearest neighbor distances, and nearest neighbor positions were analyzed.   

Flow and concentration fields in a suspension of light-guided microalgae

Many photosynthetic microorganisms display the ability known as phototaxis to move towards optimal light intensity. In suspension of microalgae Chlamydomonas Reinhardtii which are denser than water, it was recently demonstrated that phototaxis can be exploited to generate macroscopic convection flows using a localized light source that directs the horizontal motion of the cells. This is reminiscent of bioconvection which is a hydrodynamic phenomenon in suspension of motile micro-organisms heavier than water. Self-generated macroscopic convection flows arise from unstable density gradients. However, the associated concentration patterns are the most striking side of bioconvection and studies on bioconvection mainly focused on pattern formation.

In the recent light-controlled bioconvection experiments in suspensions of Chlamydomonas Reinhardtii, fluid flows were evidenced as they were used as hydrodynamic tweezers or as they induced a recirculation of the microalgae cells. In the present study, we develop a 2D-geometry fluorescence imaging system to track small passive tracers to visualize fluid flows for the first time in bioconvection in addition to the concentration field. We investigate the relationship between the bioconvection flows and their associated concentration patterns.   

Modeling large diffusio-phoretic suspensions

Phoretic particles swim by catalysing chemical reactions thus generating concentration gradients and phoretic slip flows along their surfaces. Their collective dynamics can lead to the emergence of intriguing collective dynamics and modifications in the effective properties of the suspension (e.g. viscosity and diffusivity). The numerical modeling of these reactive suspensions implies solving sequentially the Laplace and Stokes equations around many particles with prescribed surface boundary conditions, with a computational cost rapidly increasing for large numbers of particles.

We present here a novel framework for the simulation of this coupled problem. This Diffusio-phoretic Force Coupling Method is more accurate than far-field approaches, but significantly less expensive than exact methods, and is implemented in a parallelized and efficient solver to analyze the collective motion and microstructure of semi-dilute suspensions.   

Pair-wise interactions between Chlamydomonas Reinhardtii: A numerical and experimental study

Physical interactions between motile micro-organisms give rise to complex dynamics and collective motion. A better understanding of these interactions is crucial to explain the emergence of coherent motion involved in many biological phenomena from reproduction to biofilm formation. Numerical and analytical methods have been used extensively to study pair-wise interactions of micro-organisms but experimental studies are quite scarce. In this work, we use both numerical and experimental approaches to study pair-wise interactions between flagellated microorganisms. We use a multi-camera microscopy set-up to track the green alga Chlamydomonas reinhardtii, and characterize the physical interactions between two isolated cells.  A three-bead spring model is used to investigate the pair-wise interactions among puller type micro-organism and corroborate our experimental results. Our setup allows us to obtain three dimensional trajectories by which we can compare numerical and experimental results. These results are discussed in terms of relative velocity and relative swimming positions.   

Hydrodynamic interactions of active particles near surfaces

The presence of microorganisms near surfaces is a ubiquitous phenomenon in biological systems. A surface at a finite distance from active particles alters the dynamics of individual particles as well as the hydrodynamic interactions of particles due to the flows generated by each particle. In this talk, we discuss an 'active' Stokesian Dynamics approach to study the hydrodynamic interactions of suspensions of active particles near surfaces and illustrate both far-field and near-field effects on the trajectories of particles with a few simple examples. The developed method can help to establish the relationship between hydrodynamics and biological phenomena, such as biofilm formation.