Session W11: Swimming, Motility and Locomotion I

Active mixing of swimming microbes in laminar flows

We present experiments on hydrodynamic barriers that impede the motion of microswimmers in laminar flows. The flows studied are a hyperbolic flow in a cross channel, a vortex chain flow, and an oscillating channel flow. The active tracers are bacteria (bacillus subtilis) and motile eukaryotic microbes (chlamydomonas, tetraselmis and euglena).  The trajectories of these motile tracers in the flows are interpreted in terms of a theory of "swimming invariant manifolds" (SwIMs) that are manifested as one-way barriers in the fluid system. This theory is a generalization of a theory of "burning invariant manifolds" (BIMs) that have previously been shown to act as one-way barriers that block the motion of propagating reaction fronts in laminar flows.   

Emergent probability fluxes in confined microbial navigation

When the motion of a motile cell is observed closely, it appears erratic, and yet the combination of nonequilibrium forces and surfaces can produce striking examples of organization in microbial systems. While our current understanding is based on bulk systems or idealized geometries, it remains elusive how and at which length scale self-organization emerges in complex geometries. Here, using experiments, analytical and numerical calculations we study the motion of motile cells under controlled microfluidic conditions, and demonstrate that a robust topology of probability flux loops organizes active motion even at the level of a single cell exploring an isolated habitat. By accounting for the interplay of activity and interfacial forces, we find that the boundary's curvature determines the nonequilibrium probability fluxes of the motion. We theoretically predict a universal relation between fluxes and global geometric properties that is directly confirmed by experiments. Our results represent the first general description of the structure of nonequilibrium fluxes down at the single cell level opening the possibility to decipher the most probable trajectories of motile cells and may enable the design of active topological materials.   

First Passage Properties of Active Self-propelled Systems through Obstacles

Recent studies suggest that the motility phases of active matter systems depend sensitively on the structural features of their environment. In this study, we investigate the first passage properties of an active self-propelled system - a robotic bug - as it navigates through a heterogeneous environment characterised by spatially patterned densities of obstacles. We show, using extensive experiments and simulations, that different spatial patterning - as characterized by the nature of the obstacles, their number, and physical properties -  can give rise to non-trivial first passage properties. We discuss how these results can theoretically be interpreted by simple physical arguments that highlight the interplay between energy and entropy in these systems.   

Characterizing three-dimensional flow fields of free-swimming microorganisms through high-speed holographic microscopy

In understanding the locomotion of microswimmers and their interactions with the surrounding environment, one could obtain invaluable insight through characterizing the flow they induce. Previous studies have well-characterized the two-dimensional (2D) flows around numerous single microswimmers, though obtaining such measurements in three-dimensional (3D) space remains a challenging endeavor due to difficulties in performing velocimetry for 3D flows with high spatiotemporal resolution. Such flow descriptions might be crucial in understanding swimming behaviors in unconfined systems, where 3D motion becomes more apparent. In this work, we present precise measurements of the time-averaged 3D flow induced by a free-swimming Chlamydomonas reinhardtii through high-speed holographic microscopy. The flow is obtained by tracking the 3D motion of 1μm tracer particles at 500fps over thousands of the flagellar beating cycle. Our measurements capture crucial 3D features of the microorganisms' flow in their natural swimming behavior, demonstrating how potent holographic microscopy can be in imaging complex flow fields at high spatiotemporal resolutions and providing the means to elucidate the mechanism of more complex swimming behaviors.   

Optical confinement and rectification of photokinetic bacteria by feedback controlled light patterns

The bacteria Escherichia coli can be genetically engineered to swim with a light controllable speed, which turns them into the excellent tool to investigate the physics of active systems. We demonstrate a method to guide and optically confine these photokinetic bacteria towards any desired region of space. We implement a feedback loop in which the projected light pattern is determined by geometric transformations of a cell density image captured at an earlier time. With these dynamic light patterns, we are able to only boost bacteria that move in a chosen direction, which results in a directed flow of cells with an associated velocity field that can be controlled in amplitude and direction as predicted by an analytic run and tumble model. We extend the method further and use it to create large formations of confined bacteria by collecting the most motile cells and trapping them in high density and high activity formations stably over long time periods, differently from other methods that gather bacteria in low motility areas. Precisely guiding and trapping large populations of bacteria can present relevant applications in microfluidic devices, as well as it is highly interesting for the fundamental study of active matter systems and their statistical mechanic properties.   

Motility of Escherichia coli Near Biomimetic Surfaces

Many bacteria, including the well-studied Escherichia coli, transition between two modes of life: individual free-swimming cells, and surface-aggregated communities called biofilms. When a swimming E. coli approaches solid surfaces, interactions between the bacterium and the surrounding environment change, altering the bacterium’s motion. This behavior provides a measure of the interactions E. coli experiences as it transitions from free swimming to surface aggregation – a key step in early biofilm formation. Properties of the surface such as charge and viscosity can affect near-surface motility. However, the relationship between such properties and motility has yet to be described quantitatively. We aim to investigate how surface viscosity influences a bacterium’s speed, height above the surface, and the curvature of the bacterium’s trajectory. 

First, we recorded the motion of E. coli engaged in near-surface swimming above a glass coverslip using Total Internal Reflection Fluorescence (TIRF) microscopy. We developed MATLAB code to track, model, and extract dynamical measurements from the bacteria. Preliminary results matched theoretical considerations of the effects of cell-surface distance on speed and trajectory curvature. Next, we constructed biomimetic surfaces with tunable viscosity for use in near-surface motility studies. Our surface consists of a supported lipid bilayer conjugated to polystyrene microspheres through biotin-avidin binding. By adjusting the density of microspheres atop the bilayer, it is possible to control the viscosity of the colloidal surface. The viscosity can then be measured by analyzing the Brownian motion of microspheres diffusing along the bilayer. Future work will aim to measure surface viscosity as a function of microsphere density, and to use these surfaces in bacterial motility experiments.   

Markers of Chaotic Locomotion of C. elegans Swimming in Three Dimensions

Caenorhabditis elegans, more commonly known as C. elegans, are transparent nematodes approximately 1 mm long that inhabit soil in temperate environments. C. elegans have 302 neurons that are similar in form and function to that of humans, which has spiked the interest of neurological and biological communities. Time-dependent diffraction by oversampling provides information about the locomotion in the form of a single time-series. Several markers of chaos are calculated such as a broad frequency spectrum, a positive Largest Lyapunov Exponent (LLE), and the time evolution of the locomotion as visualized by Recurrence Plots (RP). The recurrence matrix is also used to visualize switching behavior time scales and to calculate Recurrence Quantification Analysis (RQA) values for comparison between different data sets. Surrogate data analysis further proves the presence of nonlinearity in the time-series. In comparison to the real worm dynamics, a simulated worm is made using a descending chain of  FitzHugh-Nagumo neurons (Singhvi, Lee et al. in our labs). Repeating the previous analysis method on the simulated worm time-series could validate the model and range of parameters necessary to invoke similar chaotic markers.   

Motility analysis of Vibrio alginolyticus after simulated microgravity

Simulated microgravity is a unique fluid environment used to mimic specific characteristics of the microgravity environment including low fluid shear, low turbulence, and lack of sedimentation. Different devices have been created to simulate microgravity, one of which is the high aspect ratio vessel (HARV) and the tool of this work. Vibrio alginolyticus, a marine pathogen, was used in this study to examine the impact of the simulated microgravity environment (HARV) on Vibrio’s motility. Vibrio’s motility has been characterized as a run-reverse-flick motility pattern. We used digital holographic microscopy (DHM) to record holograms that contain XYZT information and analyzed the recordings. Through 3D processing and analysis, we show that Vibrio’s motility patterns as described in other sources do not appear altered. Characterizing and understanding changes to Vibrio’s motility as a result of this environment are important as motility plays a key role in their chemotaxis and potentially virulence.   

Trajectory of microswimmers in square and rectangular channels

In both natural and microfluidic systems, microswimmers are often seen in confined environments. In this work we study hydrodynamic interactions between model microswimmers, namely squirmers, with confining channels using numerical simulations based on lattice Boltzmann method. The numerical approach is complemented with an analytical mathematical framework based on far field approximations. We first show that the motion of microswimmers in microfluidic channels of square and rectangular cross sections show a diverse and complex behaviour in a three dimensional channel. We propose to understand the complexity of the 3D trajectories of the microswimmers as that resulting from the superposition of two dimensional trajectories induced by a pair of confining walls. We then analyse the hydrodynamic collision process between a microswimmer and a passive particle and show that the collision results in a net displacement of the passive particle. Finally we study the hydrodynamic collision between a pair of microswimmers that occurs inside a micro-channel and the consequent modification to their trajectories.   

Microbes crossing liquid-liquid interfaces

Rod-like Bacillus subtilis swim by rotating their flagella bundles in the viscous liquid, balancing the propulsion force with the viscous drag force at a low Reynolds number environment. We investigate their motion in a quasi-two-dimensional environment with aqueous liquid-liquid interfaces, i.e., the isotropic-nematic coexistence phases of a water-based liquid crystal (LC) called lyotropic chromonic LC. Focusing on B. subtilis' interaction with the liquid-liquid interfaces, we observe that the incident angle to the interface dominantly decides if a bacterium crosses the interface or gets trapped at the interface. A bacterium with a lower incident angle, i.e., more normal to the interface, has a higher probability of crossing the interface. We observe no strong correlation between the crossing probability and the incident speed and body length. Assuming an interfacial deformation and rupture at a critical deformation, we propose a force-balance model where the propulsion force, viscous drag force, and interfacial tension are intertwined. The crossing criterion from the model supports that the incident angle may play a vital role in the crossing behavior.