Many different microswimmers propel themselves using flagella that beat periodically. The shape of the flagellar beat and swimming speed have been observed to change with fluid rheology. We quantify changes in the flagellar waveforms of Chlamydomonas reinhardtii in response to changes in fluid viscosity using (1) shape mode analysis and (2) a full swimmer simulation to analyze how shape changes affect the swimming speed and to explore the dimensionality of the shape space. By decomposing the gait into the time-independent mean shape and the time-varying stroke, we find that the flagellar mean shape substantially changes in response to viscosity, while the changes in the time-varying stroke are more subtle. Using the swimmer simulation, we quantify how the swimming speed is affected by the dimensionality of the flagellar shape reconstruction, and we show that the observed change in swimming speed with viscosity is explained by the variations in mean flagellar shape and beat frequency, while the changes in swimming speed from the different time-varying strokes are on the scale of variation between cells.
The flexibility of the bacterial flagellar hook is believed to have substantial consequences for microorganism locomotion. Using a simplified model of a rigid flagellum and a flexible hook, we show that the paths of axisymmetric cell bodies driven by a single flagellum in Stokes flow are generically helical. Phase-averaged resistance and mobility tensors are produced to describe the flagellar hydrodynamics, and a helical rod model which retains a coupling between translation and rotation is identified as a distinguished asymptotic limit. A supercritical Hopf bifurcation in the flagellar orient…
The swimming of a bead-spring chain in a viscous incompressible fluid as a model of a sperm is studied in the framework of low Reynolds number hydrodynamics. The optimal mode in the class of planar flagellar strokes of small amplitude is determined on the basis of a generalized eigenvalue problem involving two matrices which can be evaluated from the mobility matrix of the set of spheres constituting the chain. For an elastic chain with a cargo constraint for its spherical head, the actuating forces yielding a nearly optimal stroke can be determined. These can be used in a Stokesian dynamics s…
The motility of microorganisms is influenced greatly by their hydrodynamic interactions with the fluidic environment they inhabit. We show by direct experimental observation of the bi-flagellated alga Chlamydomonas reinhardtii that fluid elasticity and viscosity strongly influence the beating pattern - the gait - and thereby control the propulsion speed. The beating frequency and the wave speed characterizing the cyclical bending are both enhanced by fluid elasticity. Despite these enhancements, the net swimming speed of the alga is hindered for fluids that are sufficiently elastic. The origin…
We investigate 3-dimensional flagellar swimming in a fluid with a sparse network of stationary obstacles or fibers. The Brinkman equation is used to model the average fluid flow where a flow-dependent term, including a resistance parameter that is inversely proportional to the permeability, models the resistive effects of the fibers on the fluid. To solve for the local linear and angular velocities that are coupled to the flagellar motion, we extend the method of regularized Brinkmanlets to incorporate a Kirchhoff rod, discretized as point forces and torques along a centerline. Representing a …
Bacteria exist in a free-swimming state or in a sessile biofilm state. The transition from free-swimming to sessile mode is characterized by changes in gene expression which alter, among others,the mechanics of flagellar motility. In this paper, we propose an idealized physical model to investigate the effects of flagellar activity on the hydrodynamic interactions among a population of microswimmers. We show that decreasing flagellar activity induces a hydrodynamically-triggered transition in confined microswimmers from turbulent-like swimming to aggregation and clustering. These results sugge…
This paper addresses the physical mechanism of intermittent swimming by considering the burst-and-coast regime of fish swimming at different speeds. The burst-and-coast regime consists of a cycle with two successive phases: a phase of active undulation powered by the fish muscles followed by a passive gliding phase. Observations of real fish whose swimming gait is forced in a water flume from low to high speed regimes are performed, using a full description of the fish kinematics and mechanics. We first show that fish modulate a unique intrinsic cycle to sustain the demanded speed by modifying…
In this paper, we give formulas for the swimming of simplified two-dimensional bodies in complex fluids using the reciprocal theorem. By way of these formulas we calculate the swimming velocity due to small-amplitude deformations on the simplest of these bodies, a two-dimensional sheet, to explore general conditions on the swimming gait under which the sheet may move faster, or slower, in a viscoelastic fluid compared to a Newtonian fluid. We show that in general, for small amplitude deformations, a speed increase can only be realized by multiple deformation modes in contrast to slip flows. Ad…
Groups of beating flagella or cilia often synchronize so that neighboring filaments have identical frequencies and phases. A prime example is provided by the unicellular biflagellate Chlamydomonas reinhardtii, which typically displays synchronous in-phase beating in a low-Reynolds number version of breaststroke swimming. We report here the discovery that ptx1, a flagellar dominance mutant of C. reinhardtii, can exhibit synchronization in precise antiphase, as in the freestyle swimming stroke. Long-duration high-speed imaging shows that ptx1 flagella switch stochastically between in-phase and a…
The skill to swim fast results from the interplay between generating high thrust while minimizing drag. In front crawl, swimmers achieve this goal by adapting their inter-arm coordination according to the race pace. A transition has been observed from a catch-up pattern of coordination (i.e. lag time between the propulsion of the two arms) to a superposition pattern of coordination as the velocity increases. Expert swimmers choose a catch-up coordination pattern at low velocities with a constant relative lag time of glide during the cycle and switch to a maximum propulsion force strategy at hi…
Trajectories and conformations of uni- and multiflagellar bacteria are studied with a coarse-grained model of a cell comprised of elastic flagella connected to a cell body. The elasticities of both the hook protein (connecting cell body and flagellum) and flagella are varied. Flexibility plays contrasting roles for uni- and multiflagellar swimmers. For a uniflagellar swimmer, hook and/or flagellar buckling occurs above a critical flexibility relative to the torque exerted by the flagellar motor. Addition of a second flagellum greatly expands the parameter regime of stable locomotion, because f…
Swimming eukaryotic microorganisms such as spermatozoa, algae and ciliates self-propel in viscous fluids using travelling wave-like deformations of slender appendages called flagella. Waves are predominant because Purcell's scallop theorem precludes time-reversible kinematics for locomotion. Using the calculus of variations on a periodic long-wavelength model of flagellar swimming, we show that the planar flagellar kinematics maximising the time-averaged propulsive force for a fixed amount of energy dissipated in the surrounding fluid correspond for all times to waves travelling with constant …
At the millimeter scale and in the intermediate Reynolds number (Re) regime, the midge and mosquito larvae can reach swimming speeds of more than one body length per cycle performing a "figure-of-8" gait, in which their elongated bodies periodically bend nearly into circles and then fully unfold. To elucidate the propulsion mechanism of this cycle of motion, we conducted a 3D numerical study which investigates the hydrodynamics of undergoing the prescribed kinematics. Novel propulsion mechanisms, such as modulating the body deformation rate to dynamically increase the maximum net propulsion fo…
The presence of a nearby boundary is likely to be important in the life cycle and evolution of motile flagellate bacteria. This has led many authors to employ numerical simulations to model near-surface bacterial motion and compute hydrodynamic boundary effects. A common choice has been the method of images for regularized Stokeslets (MIRS); however, the method requires discretization sizes and regularization parameters that are not specified by any theory. To determine appropriate regularization parameters for given discretization choices in MIRS, we conducted dynamically similar macroscopic …
Flagellar motility is critical to natural and many forms of assisted reproduction. Rhythmic beating and wave propagation by the flagellum propels sperm through fluid and enables modulation between penetrative progressive motion, activated side-to-side yaw and hyperactivated motility associated with detachment from epithelial binding. These motility changes occur in response to the properties of the surrounding fluid environment, biochemical activation state, and physiological ligands, however a parsimonious mechanistic explanation of flagellar beat generation that can explain motility modulati…
University of Pennsylvania（宾夕法尼亚大学）；National Institute for Mathematical Sciences（韩国数学科学国立研究所）；Chung-Ang University（中央大学）；University of Cincinnati（辛辛那提大学）
The behavior of flagellated bacteria swimming in non-Newtonian media remains an area with contradictory and conflicting results. We report on the behavior of wild-type and smooth-swimming E. coli in Newtonian, shear thinning and viscoelastic media, measuring their trajectories and swimming speed using a three dimensional real-time tracking microscope. We conclude that the speed enhancement in Methocel solution at higher concentration is due to shear-thinning and an analytical model is used to support our experimental result. We argue that shear-induced normal stresses reduce the wobbling behav…
Inviscid computational results are presented on a self-propelled swimmer modeled as a virtual body combined with a two-dimensional hydrofoil pitching intermittently about its leading edge. Lighthill (1971) originally proposed that this burst-and-coast behavior can save fish energy during swimming by taking advantage of the viscous Bone-Lighthill boundary layer thinning mechanism. Here, an additional inviscid Garrick mechanism is discovered that allows swimmers to control the ratio of their added mass thrust-producing forces to their circulatory drag-inducing forces by decreasing their duty cyc…
Microorganisms are rarely found in Nature swimming freely in an unbounded fluid. Instead, they typically encounter other organisms, hard walls, or deformable boundaries such as free interfaces or membranes. Hydrodynamic interactions between the swimmer and nearby objects lead to many interesting phenomena, such as changes in swimming speed, tendencies to accumulate or turn, and coordinated flagellar beating. Inspired by this class of problems, we investigate locomotion of microorganisms near deformable boundaries. We calculate the speed of an infinitely long swimmer close to a flexible surface…
In this paper we study the motion of three linked ellipses moving through a viscous fluid in two dimensions. The angles between the ellipses change with time in a specified manner (the gait) and the resulting time varying configuration is similar to the appearance of a swimming leech. We simulate the motion using the particle method Smoothed Particle Hydrodynamics (SPH) which we test by convergence studies and by comparison with the inviscid results of Kanso et al. (2005) and the viscous results of Eldredge (2006, 2007, 2008). We determine how the average speed and power output depends on the …
We use high-speed x-ray imaging to reveal how a small (~10cm) desert dwelling lizard, the sandfish (Scincus scincus), swims within a granular medium [1]. On the surface, the lizard uses a standard diagonal gait, but once below the surface, the organism no longer uses limbs for propulsion. Instead it propagates a large amplitude single period sinusoidal traveling wave down its body and tail to propel itself at speeds up to ~1.5 body-length/sec. Motivated by these experiments we study a numerical model of the sandfish as it swims within a validated soft sphere Molecular Dynamics granular media s…
Many small organisms self-propel in viscous fluids using travelling wave-like deformation of their bodies or appendages. Examples include small nematodes moving through soil using whole-body undulations or spermatozoa swimming through mucus using flagellar waves. When self-propulsion occurs in a non-Newtonian fluid, one fundamental question is whether locomotion will occur faster or slower than in a Newtonian environment. Here we consider the general problem of swimming using small-amplitude periodic waves in a viscoelastic fluid described by the classical Oldroyd-B constitutive relationship. …
Swimming cells and microorganisms are as diverse in their collective dynamics as they are in their individual shapes and propulsion mechanisms. Even for sperm cells, which have a stereotyped shape consisting of a cell body connected to a flexible flagellum, a wide range of collective dynamics is observed spanning from the formation of tightly packed groups to the display of larger-scale, turbulence-like motion. Using a detailed mathematical model that resolves flagellum dynamics, we perform simulations of sperm suspensions containing up to 1000 cells and explore the connection between individu…
The effects of temperature and viscosity on the metachronal swimming of crustaceans
Center for Fluid Mechanics, School of Engineering, Brown University（布朗大学工程学院流体力学中心）；Department of Mechanical and Aerospace Engineering, Case Western Reserve University（凯斯西储大学机械与航空航天工程系）
Colonies of the green alga $Volvox$ are spheres that swim through the beating of pairs of flagella on their surface somatic cells. The somatic cells themselves are mounted rigidly in a polymeric extracellular matrix, fixing the orientation of the flagella so that they beat approximately in a meridional plane, with axis of symmetry in the swimming direction, but with a roughly 15 degree azimuthal offset which results in the eponymous rotation of the colonies about a body-fixed axis. Experiments on colonies held stationary on a micropipette show that the beating pattern takes the form of a sympl…
In many biological systems, microorganisms swim through complex polymeric fluids, and usually deform the medium at a rate faster than the inverse fluid relaxation time. We address the basic properties of such life at high Deborah number analytically by considering the small-amplitude swimming of a body in an arbitrary complex fluid. Using asymptotic analysis and differential geometry, we show that for a given swimming gait, the time-averaged leading-order swimming kinematics of the body can be expressed as an integral equation on the solution to a series of simpler Newtonian problems. We then …
Department of Mechanical Engineering, Penn State University（宾夕法尼亚州立大学机械工程系）
In this work we developed a mathematical model and a simulation platform for a fish-inspired robotic template, namely Magnetic, Modular, Undulatory Robotics ($μ$Bots). Through this platform, we systematically explored the effects of design and fluid parameters on the swimming performance via reinforcement learning. The mathematical model was composed of two interacting subsystems, the robot dynamics and the hydrodynamics, and the hydrodynamic model consisted of reactive components (added-mass and pressure forces) and resistive components (drag and friction forces), which were then nondimension…
Peritrichous bacteria such as Escherichia coli swim in viscous fluids by forming a helical bundle of flagellar filaments. The filaments are spatially distributed around the cell body to which they are connected via a flexible hook. To understand how the swimming direction of the cell is determined, we theoretically investigate the elastohydrodynamic motility problem of a multi-flagellated bacterium. Specifically, we consider a spherical cell body with a number N of flagella which are initially symmetrically arranged in a plane in order to provide an equilibrium state. We analytically solve the…
Microswimmers in nature often experience spatial gradients of viscosity. In this work we develop theoretical results for the dynamics of active particles, biological or otherwise, swimming through viscosity gradients. We model the active particles using the squirmer model, and show how viscosity gradients lead to viscotaxis for squirmers, and how the effects of viscosity gradients depend on the swimming gait of the microswimmers. We also show how such gradients in viscosity can be used to control active particles and suggest a mechanism to sort them based on their swimming style.
Optimal gait design is important for micro-organisms and micro-robots that propel themselves in a fluid environment in the absence of external force or torque. The simplest models of shape changes are those that comprise a series of linked-spheres that can change their separation and their sizes. We examine the dynamics of three existing linked-sphere types of modeling swimmers in low Reynolds number Newtonian fluids using asymptotic analysis, and obtain their optimal swimming strokes by solving the Euler-Lagrange equation using the shooting method. The numerical results reveal that (1) with t…
To explore and react to their environment, living micro-swimmers have developed sophisticated strategies for locomotion - in particular, motility with multiple gaits. To understand the physical principles associated with such a behavioural variability,synthetic model systems capable of mimicking it are needed. Here, we demonstrate bimodal gait switching in autophoretic droplet swimmers. This minimal experimental system is isotropic at rest, a symmetry that can be spontaneously broken due to the nonlinear coupling between hydrodynamic and chemical fields, inducing a variety of flow patterns tha…
Improving the numerical method of fish autonomous swimming behavior in complex environments is of great significance to the optimization of bionic controller,the design of fish passing facilities and the study of fish behavior.This work has built a fish autonomous swimming simulation platform,which adapts the high-precision IB-LBM to simulate the dynamic process of the interaction between the fish and the flow field in real time,and realizes the fish brain motion control through the SAC deep reinforcement learning algorithm.More importantly,in view of the poor generalization of the existing si…
Simulations of undulatory swimming in viscoelastic fluids with large amplitude gaits show concentration of polymer elastic stress at the tips of the swimmers.We use a series of related theoretical investigations to probe the origin of these concentrated stresses. First the polymer stress is computed analytically at a given oscillating extensional stagnation point in a viscoelastic fluid. The analysis identifies a Deborah number (De) dependent Weissenberg number (Wi) transition below which the stress is linear in Wi, and above which the stress grows exponentially in Wi. Next, stress and velocit…
