Bulletin of the American Physical Society
66th Annual Meeting of the APS Division of Fluid Dynamics
Volume 58, Number 18
Sunday–Tuesday, November 24–26, 2013; Pittsburgh, Pennsylvania
Session M21: Biofluids: Locomotion IX  Bacteria and Microswimmers I 
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Chair: Henry Fu, University of Nevada  Reno Room: 316 
Tuesday, November 26, 2013 8:00AM  8:13AM 
M21.00001: Induced Diffusion of Tracers in a Bacterial Suspension: Theory and Experiments Rodrigo Soto, Gaston Mino, Jocelyn Dunstan, Eric Clement, Annie Rousselet The induced diffusion of tracers in a bacterial suspension is studied at low bacterial concentrations. Considering the swimmertracer hydrodynamic interactions at lowReynolds number and using a kinetic theory approach, it is shown that the induced diffusion coefficient is proportional to the swimmer concentration, their mean velocity and a coefficient $\beta$. The coefficient scales as the tracerswimmer cross section times the mean square displacement produced by single scatterings. Considering simple swimmer models it is shown that $\beta$ increases for decreasing swimming efficiencies. Close to solid surfaces the swimming efficiency degrades and, consequently, the induced diffusion increases. Experiments on W wildtype {\em Escherichia coli} in a HeleShaw cell, under buoyant conditions, are performed to measure the induced diffusion on tracers near surfaces. The modification of the suspension pH varies the swimmers' velocity in a wide range allowing to extract the $\beta$ coefficient with precision. It is found that that the solid surfaces modify the induced diffusion: decreasing the confinement height of the cell, $\beta$ increases by a factor 4. The theoretical model reproduces this increase although there are quantitative differences, due to the simplified model. [Preview Abstract] 
Tuesday, November 26, 2013 8:13AM  8:26AM 
M21.00002: Rheological and boundary effects on microswimmers Thomas MontenegroJohnson, Daniel Loghin, David Smith Two important environmental factors impacting cell motility are the rheological properties of the surrounding fluid and the presence of boundaries. In this talk we will present simulations that explore the relationship between microswimmer, fluid rheology and boundary features, with a particular emphasis on the example of human sperm. Human sperm must navigate the labyrinthine structure of human fallopian tubes, actively bending their flagella in order to propel themselves through physiological mucus. Sperm trajectories are greatly affected by boundaries, scattering over features such as steps and ripples. We present simulations of scattering spermlike swimmers in confined geometries, comparing these results to experiments of swimmers in microchannels. The rheological properties of mucus also affect sperms' ability to penetrate. Using the method of femlets, a new finite element technique entailing an immersed force representation of the swimmer with a bodyfitted mesh, we present novel physical mechanisms through which shearthinning, an important property of physiological mucus affects microscopic swimmers. In particular, we show that these effects are sensitive to the swimming stroke employed, and present example reciprocal swimmers that violate Purcell's Scallop Theorem. [Preview Abstract] 

M21.00003: ABSTRACT WITHDRAWN 
Tuesday, November 26, 2013 8:39AM  8:52AM 
M21.00004: The signatures of microstructure in swimming properties of microorganisms in heterogeneous media Mehdi Jabbarzadeh, Henry Fu Many swimming microorganisms move through complex bioenvironments. Some of these environments, such as mucuses, contain a network of filaments with features at lengthscales comparable to the swimmers. In order to understand the effects of these heterogeneous microstructures on the swimming velocity of microorganism, we use Higdon's Slender Body Theory to study the hydrodynamic interaction between a Golestanian threesphere swimmer and filaments. We find that in spatially varying background flows, there is an optimal length for the filament segments in Higdon's Slender Body Theory, and that the effect on swimming velocity is wellapproximated by the Stokeslet contribution to the flow. We consider the effect of media composed of many such filaments. For isotropic media, the average change of the swimming velocity is determined by the density of the medium, while the variance of the swimming velocity depends on the filament structure through its densitydensity correlation function. The dependence of the variance on the medium can be understood by relating lengthscales of the medium microstructure to lengthscales of the swimmer's velocity field. [Preview Abstract] 
Tuesday, November 26, 2013 8:52AM  9:05AM 
M21.00005: Nutrient uptake in a suspension of squirmers Shunsuke Kajiki, Yohsuke Imai, Takami Yamaguchi, Takuji Ishikawa Although microorganisms exist everywhere and significantly influence our life, little is known about the mass transport in suspensions of microorganisms. The aim of this study is to analyze the effect of the swimming motion on the nutrient uptake. In this study, we propose a discrete model of concentration field of nutrients in a microbial suspension, and simulate the nutrient uptake by model microorganisms. We modeled a microorganism as a squirmer, which swims by generating the tangential velocity on its surface. The hydrodynamic interactions between squirmers were calculated by Stokesian dynamics method. We first analyzed the uptake ratio of a squirmer in an infinite domain without any background flow, which agreed well with former study by Magar et al.(2003). Then, we investigated nutrient uptake process in an infinite suspension of squirmers with the volume ratio of 0.010.35. The results showed that the suspension uptake rate was strongly dependent on the volume ratio of squirmers, the swimming mode of squirmers and Peclet number. These results are important in understanding the transport phenomena in a microbial suspension. [Preview Abstract] 
Tuesday, November 26, 2013 9:05AM  9:18AM 
M21.00006: Hydrodynamic interaction of bacterial flagella  flagellar bundling Sookkyung Lim Flagellar bundling is an important aspect of locomotion in bacteria such as Escherichia coli. To study the hydrodynamic behavior of helical flagella, we present a computational model that is based on the geometry of the bacterial flagellar filament at the micrometer scale. We consider two model flagella, each of which has a rotary motor at its base with the rotation rate of the motor set at 100 Hz. Bundling occurs when both flagella are lefthanded helices turning counterclockwise (when viewed from the nonmotor end of the flagellum looking back toward the motor) or when both flagella are righthanded helices turning clockwise. Helical flagella of the other combinations of handedness and rotation direction do not bundle. In this work we use the generalized immersed boundary method combined with the unconstrained Kirchhoff rod theory, which allows us to study the complicated hydrodynamics of flagellar behavior. This is a joint work with Charlie Peskin at NYU. [Preview Abstract] 
Tuesday, November 26, 2013 9:18AM  9:31AM 
M21.00007: Hydrodynamic model of bacterial tumbling near a nonslip surface Jian Sheng, Mehdi Molaei To swim forward, wild type \textit{Escherichia coli} bacteria rotate their helical flagella CCW to form a bundle; to tumble, one or more flagella rotate CW to initiate flagella unbundling and polymorphic transformation that leads to a significant change in cell orientation in comparison to original swimming direction. These random change of direction increases bacterial dispersion and also is long speculated to be a mechanism for perichtricous bacteria to escape from a surface. Our recent experimental results show that the tumbling frequency is substantially suppressed near a solid surface by 50{\%}, and the bacterium tends to start a new run in the direction parallel to the surface. This suppression occurs at two cell length (including flagella) away from the surface whereby steric hindrance plays less significant role. Here we propose an analytical model based on hydrodynamic interaction between flagella and the solid surface. We utilize Slender Body Theory combined with the image system of the singularities for the Stokeflow to quantify the flow around the bacterial flagella in the presence of a noslip surface. The model includes two nonidentical rigid helical flagella representing a bundle and single flagellum. We have showed that in the bulk, a repulsive force among flagella initiates the unbundling and consequently tumbling; however, in presence of a solid surface, the force is strongly mitigated that stabilize the bundle and suppress the tumbling. [Preview Abstract] 
Tuesday, November 26, 2013 9:31AM  9:44AM 
M21.00008: Swimming of a Ciliated Microorganism Hanliang Guo, Eva Kanso We propose a 2D model to consider the locomotion of a ciliated microorganism in a viscous fluid. The model consists of a circular body whose boundary is covered by a finite number of cilia. Stokes paradox does not hold due to the selfpropelling nature of the organism. Using a regularized Stokeslet method, we determine numerically the timedependent swimming motion for prescribed kinematics (undulatory beat) of the individual cilium. Phase differences between neighboring cilia result in metachronal waves characteristic of biological cilia. We compare our results based on the discrete cilia approach with the envelope model proposed by JR Blake. We then study the net locomotion as function of the metachronal wave. We find that, for a given geometry and cilia density, there is an optimal wave number (phase difference) for locomotion in terms of velocity of propulsion and efficiency. [Preview Abstract] 
Tuesday, November 26, 2013 9:44AM  9:57AM 
M21.00009: Collective Swimming in a Suspension of Ellipsoidal Squirmers Kohei Kyoya, Daiki Matsunaga, Yohsuke Imai, Takami Yamaguchi, Takuji Ishikawa Some recent research efforts have demonstrated the importance of biomechanics in understanding certain aspects of microorganism behaviors such as locomotion and collective motions of cells. However, former studies had problems in accurately computing manybody interaction of model microorganisms. In this study, we propose a boundary element method, based on the doublelayer representation, for calculating interactions of manybody swimmers in Stokes flow regime. The proposed method allows us to analyze a large system size that could not be handled before. The model microorganism is assumed to be ellipsoid and propels itself by generating tangential velocities on its surface. Two types of microorganisms were modeled by varying the surface velocity; one is a ``puller'' which has the thrustgenerating apparatus in front of the body such as {\sl Chlamydomonas}, and the other is a ``pusher'' which has the thrust behind the body such as bacteria or spermatozoa. We then analyze interactions of 100 pullers or pushers. In both cases, some sorts of collective swimming were observed. In particular, pullers and neutral swimmers created large clusters and generated coherent structures. [Preview Abstract] 
Tuesday, November 26, 2013 9:57AM  10:10AM 
M21.00010: Contribution of cell body to the thrust production of flagellate bacteria Bin Liu, Thomas R. Powers, Kenneth S. Breuer We trace individual motile microorganisms using a digital 3D tracking microscope in which the microscope stage follows the motion of the target. Using this technology, we not only trace a single cell over extended duration but also obtain the cell kinematics with high spatial and temporal resolution. We apply this tracking microscope to a study of Caulobacter crescentus, a bacterium that moves up to 100 microns (or 50 body lengths) per second and reverses its direction of motion by switching the rotation direction of its single helical flagellum. We show that when the cell reverses the rotation direction of the righthanded flagellum, e.g., switching from CW (a pusher) to CCW (a puller), its cellkinematics is not completely reversible. In case of a puller, the cell almost spins along its long axis. However, in case of a pusher, besides spinning, the cell body precesses along its swimming direction, following a helical trajectory. These two types of cellkinematics contribute to different cell motilities: the pusher rotates slower for the same swimming speed. We present a resistive force theory to account for this behavior, and by computing the torque on the cell body, we show that the finite precession angle of the bacterial pusher is optimized for swimming with fixed torque. [Preview Abstract] 
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