Bulletin of the American Physical Society
62nd Annual Meeting of the APS Division of Fluid Dynamics
Volume 54, Number 19
Sunday–Tuesday, November 22–24, 2009; Minneapolis, Minnesota
Session HW: Swimming IV: Micro-organisms I |
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Chair: Roman Stocker, Massachusetts Institute of Technology Room: 208A-D |
Monday, November 23, 2009 10:30AM - 10:43AM |
HW.00001: A microfluidic study of biofilms on topographically complex surfaces William Durham, Alberto Leombruni, Matthew McKinley, Anna Shcherbina, Roman Stocker A biofilm forms when bacteria attach to a surface and secrete sticky polymeric substances. Several factors control biofilm formation and maintenance, including cell motility, erosion by fluid shear, bacterial growth, nutrient diffusion, and surface properties. In particular, the surface is often topographically complex and allows heterogeneous microenvironments to develop. We studied how these processes influence biofilm dynamics using a patterned microfluidic channel, composed of an array of cylinders of random diameter and position. We tracked the evolution of a biofilm of fluorescently labeled \textit{Escherichia coli} cells under flow over 48 hours and used periodic injections of microspheres to quantify the flow field. The biofilm first forms as a front that travels three orders of magnitude slower than the mean fluid velocity, then breaks into a series of patches separated by preferential flow channels. This striking channelization was rationalized using a simple network model. A full understanding of these dynamics will be relevant to problems in environmental and medical sciences. [Preview Abstract] |
Monday, November 23, 2009 10:43AM - 10:56AM |
HW.00002: ABSTRACT HAS BEEN MOVED TO AE.00010 |
Monday, November 23, 2009 10:56AM - 11:09AM |
HW.00003: Investigating bacteria-surface interactions with microfluidics and Digital Holographic Microscopy Harsh Agarwal, Michael Barry, Roman Stocker, Jian Sheng Quantitative data of swimming characteristics of bacteria in the shear flow adjacent to a surface are crucial for understanding cell attachment and detachment, and thus biofilm formation. We combined microfluidics and holography to expose \textit{Escherichia coli} AW405 to a carefully controlled flow environment and visualize their movement in three dimensions. We investigated wall shear rates up to 200 (1/s) and recorded holograms at 40X magnification and 15fps for several minutes. Three-dimensional locations and orientations of bacteria were extracted from numerically reconstructed images. We obtained thousands of 3D trajectories over a sample volume of 380$\times $380$\times $200 $\mu $m, with a resolution of 0.2 $\mu $m in the two in-plane directions and 1 $\mu $m in the out-of-plane direction. Preliminary results revealed a range of behaviors, including circular trajectories near surfaces and migration normal to the wall. We expect that ongoing analysis will provide robust statistics of wall effects on bacterial motility. Sponsored by NIH (1-R21-EB008844-01) and NSF (CBET-0844647, DBI-0852875) [Preview Abstract] |
Monday, November 23, 2009 11:09AM - 11:22AM |
HW.00004: Dynamics of Enhanced Tracer Diffusion in Suspensions of Swimming Microorganisms J.P. Gollub, J.S. Guasto, K.C. Leptos, A.I. Pesci, R.E. Goldstein We observe and statistically quantify the enhanced transport of passive tracer particles in suspensions of swimming microalgae, Chlamydomonas reinhardtii. These bi-flagellated, single-celled eukaryotes (10 $\mu$m diameter) swim with a breast-stroke motion of their flagella at speeds of about 100 $\mu$m/s and exhibit a heterogeneous trajectory shapes. Fluorescent tracer particles (2 $\mu$m diameter) allowed us to quantify the enhanced mixing caused by the swimmers, which is relevant to marine ecology. As the swimmer concentration increases, the probability density functions (PDFs) of tracer displacements develop strong exponential tails, and the Gaussian core broadens; the diffusivity grows linearly with concentration. For a given swimmer concentration, the displacement PDFs show self-similar behavior and diffusive scaling in time. High-speed imaging of tracer-swimmer interactions demonstrates the importance of flagellar beating in creating oscillatory flows that exceed Brownian motion out to about 5 cell radii from the swimmers.\footnote{K.C. Leptos et al., submitted to Phys. Rev. Lett (2009)} [Preview Abstract] |
Monday, November 23, 2009 11:22AM - 11:35AM |
HW.00005: Bacteria swimming in shear Marcos, Roman Stocker The watery habitat of bacteria is typically in motion, exposing cells to fluid shear and thus to a viscous torque. By tracking individual bacteria exposed to a range of shear rates in microfluidic channels, we find that shear alters bacterial swimming patterns and in particular reduces movement across streamlines. This results from the bacteria undergoing Jeffery orbits, which bias cell orientation in the direction of the flow and hamper cross-streamline swimming. We speculate that this could significantly hinder chemotaxis and the quest for nutrients. A model based on resistive force theory is in good agreement with the observations. This process is a purely passive hydrodynamic effect. Further experiments suggest that bacteria do not actively respond to shear: nature has apparently not deemed it worthwhile to develop a shear sensor at the micrometer scale. [Preview Abstract] |
Monday, November 23, 2009 11:35AM - 11:48AM |
HW.00006: Bacteria foraging in turbulent waters John Taylor, Wenbo Tang, Roman Stocker Marine bacteria are the Ocean's recyclers, contributing to as much as 50\% of the productivity of the marine food web. Bacteria forage on patches of dissolved nutrients using chemotaxis, the ability to swim up chemical gradients. As turbulence is ubiquitous in the Ocean, it is important to understand how turbulent flow conditions affect bacterial foraging. We used three-dimensional, isotropic direct numerical simulations coupled with a bacterial transport equation to address this problem. After the flow is continuously forced until it reaches a steady state, microscale nutrient patches are injected into the turbulent flow, and stirring produces thin nutrient filaments. Two populations of bacteria compete against each other: one population is motile and chemotactic (`active'), the other is non-motile (`passive'). The distribution of both populations is initially uniform. Chemotaxis allows active bacteria to cluster near the center of the nutrient filaments, increasing their nutrient uptake relative to passive bacteria. Increasing the turbulence intensity increases the short-term chemotactic advantage by quickly producing large gradients in the nutrient concentration, but also leads to rapid mixing of the nutrient field, which makes the chemotactic advantage short-lived. The results suggest that the evolutionary advantage of chemotaxis, based on the increase in nutrient uptake relative to the energetic cost of swimming, strongly depends on the turbulence level. [Preview Abstract] |
Monday, November 23, 2009 11:48AM - 12:01PM |
HW.00007: Strain Variants in Swimming Characteristics of a Predatory Algae Species Jian Sheng, Joseph Katz, J. Adolf, Allen Place Digital holographic microscopic cinematography is used for measuring the 3D, time resolved, swimming behavior of toxic and non-toxic strains of the marine dinoflagellates\textit{ Karlodinium veneficum}. The experiments are performed in a 3$\times $3 mm square cuvette at densities of $\sim $150,000 cells/ml, and holograms are recorded at 120fps and 20X magnification for 12-20s. In each case, we simultaneously track 200-500 cells in the 3mm deep sample, at a spatial resolution of 0.4$\times $0.4$\times $2 $\mu$m. Results show that all strains prefer vertical migration during phototrophic growth and localized foraging in response to prey. Strains capable of swimming in both left and right hand helices show stronger tendency towards vertical motion than right handed strains. Swimming-induced dispersion computed from Lagrangian trajectories corroborates the observed migration trends, and suggests a mechanism for predation-induced cell aggregation into dense bloom. Velocity spectra and conditional sampling of swimming modes will also be presented to elucidate locomotion of dinoflagellates. [Preview Abstract] |
Monday, November 23, 2009 12:01PM - 12:14PM |
HW.00008: Fluid dynamics of phytoplankton with spines in unsteady shear flows Hoa Nguyen, Lee Karp-Boss, Peter Jumars, Lisa Fauci Spines and other thin projections from cell surfaces literally expand the volume of fluid with which a cell interacts and may provide effective levers on which the flow can act. We use an immersed boundary formulation to solve the coupled phytoplankton-fluid system to predict the 3D trajectories of the cells within a background flow. We examine the effect of spines on the trajectories, along with the effect of stiffness properties of these spines. [Preview Abstract] |
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