Bulletin of the American Physical Society
68th Annual Meeting of the APS Division of Fluid Dynamics
Volume 60, Number 21
Sunday–Tuesday, November 22–24, 2015; Boston, Massachusetts
Session G23: Biofluids: Active Fluids III |
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Chair: Enkeleida Lushi, Brown University Room: 300 |
Monday, November 23, 2015 8:00AM - 8:13AM |
G23.00001: Emergent dynamics and phase behavior of interacting ellipsoid micro-swimmers Enkeleida Lushi Suspensions of self-propelling ellipse particles are known to display distinct phases depending on the density and particle aspect ratio: dilute gas, jammed state, swarms, bionematic state, turbulence or lanes. Each of these non-equilibrium phases exhibits distinct characteristics. Recent studies on the other hand have shown that the dynamics observed in bacterial suspensions can be better explained when accounting also for the disturbance fluid flow generated by the swimmers and their interactions through it. Using numerical simulations, we show that including the fluid interactions in the dynamics of ellipse motile particles modifies the system dynamics, e.g. the clustering of the swimmers and other physical characteristics. We show that the phase state diagram is significantly altered depending on the type of swimmer (``pusher'' or ``puller'' vs. ``mover'') as well the swimmer density and aspect ratio. [Preview Abstract] |
Monday, November 23, 2015 8:13AM - 8:26AM |
G23.00002: Stability of localized bioconvection patterns of Euglena suspensions Makoto Iima, Takayuki Yamaguchi Suspension of {\it Euglena gracilis} forms localized convection cells when it is illuminated form below with strong light intensity. Two elementary localized structures are known. One consists of a single region of high number density of the microorganism sandwiched with a pair of convection cells (bioconvection unit) and the other is a localized traveling wave. Measurements of the flux of the number density suggests that the photomovement due to light gradient plays an important role in generating localized convection cells. We proposed a hydrodynamic model incorporating the effect, and succeed in reproducing bioconvection unit, which can be characterized as steady solutions of the proposed model. Bifurcation structure of the solutions are analyzed. The bistable region due to the subcritical bifurcation from trivial state and folding of branch due the saddle-node bifurcation is observed. The stability analysis in the bistable region revealed that the most unstable mode represents a sweep of number density to the central part and reducing the size of the convection cells, which leads the unstable solution to the stable steady solution representing bioconvection unit. [Preview Abstract] |
Monday, November 23, 2015 8:26AM - 8:39AM |
G23.00003: Symmetry-breaking phase-transitions in highly concentrated semen Franck Plouraboué, Adama Creppy, Olivier Praud, Xavier Druart, Sébastien Cazin, Hui Yu, Pierre Degond New experimental evidence of self-motion of a confined active suspension is presented. Depositing fresh semen sample in an annular shaped micro-fluidic chip leads to a spontaneous rotation motion of the fluid at sufficiently large sperm concentration. The rotation occurs unpredictably clockwise or counterclockwise and is robust and stable. Furthermore, for highly active and concentrated semen, richer dynamics can occur such as self-sustained or damped rotation oscillations. Experimental results obtained with systematic dilution provide a clear evidence of a phase transition toward collective motion associated with local alignment of spermatozoa akin to the Vicsek model. A macroscopic theory based on previously derived Self-Organized Hydrodynamics (SOH) models is adapted to this context and provides predictions consistent with the observed stationary motion. [Preview Abstract] |
Monday, November 23, 2015 8:39AM - 8:52AM |
G23.00004: Flock on a chip Denis Bartolo, Nicolas Desreumaux We will show how to motorize colloidal particles capable of sensing the orientation of their neighbors and how to handle them in microfluidic chips. These populations of colloidal rollers display non-equilibrium transitions toward swarming or swirling motion depending on the system geometry . After characterizing these emergent patterns we will quantitatively describe them by means of an hydrodynamic theory of polar active liquids. [Preview Abstract] |
Monday, November 23, 2015 8:52AM - 9:05AM |
G23.00005: Using a stochastic field theory to understand group behavior in microswimmer suspensions Patrick Underhill, Yuzhou Qian, Peter Kramer Active suspensions of microswimmers appear both in natural biological systems (e.g. bacteria or algae) and in synthetic systems. Even without external forcing they are out of equilibrium, which gives rise to interesting properties in both small and large concentrations of the particles. These properties have been observed in experiments as well as simulation/modeling approaches. It is important to understand how hydrodynamic interactions between active swimmers cause and/or alter the suspension properties including enhanced transport and mixing. One of the most successful approaches has been a mean field theory. However, in some situations the mean field theory makes predictions that differ significantly from experiments and direct (agent or particle based) simulations. There are also some quantities that cannot be calculated by the mean field theory. In this talk, we will describe our new approach which uses a stochastic field to overcome the limitations of the mean field assumption. It allows us to calculate how interactions between organisms alter the correlations and mixing in conditions where the mean field theory cannot. [Preview Abstract] |
Monday, November 23, 2015 9:05AM - 9:18AM |
G23.00006: Hydrodynamic analysis and mechanisms of ciliary beating Ashok Sangani, Kenneth Foster The scaffold of a cilium or eukaryotic flagellum, known as the axoneme, consists of nine microtubule doublets surrounding a pair of singlet microtubules. Attached to each doublet are periodically-spaced dynein motors that use energy from ATP hydrolysis to exert force on the neighboring doublet causing it to slide away from the cell body. In spite of the several theories that have been put forward over the last several decades to explain how these motors work collectively to produce steady beating this question remains unresolved: we shall show that the forces generated during the beating as determined from the detailed hydrodynamic analysis are inconsistent with the predictions of the existing theories. We shall also use the experimental data available in the literature to present empirical results for the beat properties, i.e. the frequency, amplitude, wavelength, and energy dissipation, as functions of ATP concentration and fluid viscosity. The power dissipated and the energy per wavelength are approximately the same independent of the viscosity of the fluid and the ATP concentration. We use these observations to suggest a new hypothesis regarding how the cilia beat. [Preview Abstract] |
Monday, November 23, 2015 9:18AM - 9:31AM |
G23.00007: Emergence of collective motion in suspensions of swimming cells Maria Chiara Roffin, Petr Denissenko, Vasily Kantsler Collective motion is one of the most fascinating manifestations of self-organization in non-equilibrium systems. The phenomena emerges with the increase in concentration of motile individuals ranging from molecular motors to large animals like fish and humans. We have studied the suspension of swimming sperm cells in a microfluidic device which gradually concentrates motile cells in the region of interest. The onset of collective motion is identified by investigating correlations of fluid velocity and image brightness associated with the cell orientation. Cell concentration and the noise parameter are varied to switch on/off the collective interaction. The level of noise is controlled by adjusting the cell motility which depends on the temperature in the microfluidic chip. Fluid velocity is measured by tracing passive fluorescent beads in the suspension. [Preview Abstract] |
Monday, November 23, 2015 9:31AM - 9:44AM |
G23.00008: Aerotactic Cell Density Variations in Bacterial Turbulence Vicente Fernandez, Steven Smriga, Filippo Menolascina, Roberto Rusconi, Roman Stocker Concentrated suspensions of motile bacteria such as \textit{Bacillus subtilis} exhibit group dynamics much larger than the scale of an individual bacterium, visual similar to high Reynolds number turbulence. These suspensions represent a microscale realization of active matter. Individually, \textit{B. subtilis} are also aerotactic, and will accumulate near oxygen sources. Using a microfluidic device for generating oxygen gradients, we investigate the relationship between individuals' attraction to oxygen and the collective motion resultant from hydrodynamic interactions. We focus on changes in density revealed by a fluorescently labeled sub-population of \textit{B. subtilis} in the dense suspension. This approach allows us to examine changes in density during the onset of collective motion as well as fully developed bacterial turbulence. [Preview Abstract] |
Monday, November 23, 2015 9:44AM - 9:57AM |
G23.00009: A Rules-Based Simulation of Bacterial Turbulence Maxwell Mikel-Stites, Anne Staples In sufficiently dense bacterial populations (\textgreater 40{\%} bacteria by volume), unusual collective swimming behaviors have been consistently observed, resembling von Karman vortex streets. The source of these collective swimming behavior has yet to be fully determined, and as of yet, no research has been conducted that would define whether or not this behavior is derived predominantly from the properties of the surrounding media, or if it is an emergent behavior as a result of the ``rules'' governing the behavior of individual bacteria. The goal of this research is to ascertain whether or not it is possible to design a simulation that can replicate the qualitative behavior of the densely packed bacterial populations using only behavioral rules to govern the actions of each bacteria, with the physical properties of the media being neglected. The results of the simulation will address whether or not it is possible for the system's overall behavior to be driven exclusively by these rule-based dynamics. In order to examine this, the behavioral simulation was written in MATLAB on a fixed grid, and updated sequentially with the bacterial behavior, including randomized tumbling, gathering and perceptual sub-functions. If the simulation is successful, it will serve as confirmation that it is possible to generate these qualitatively vortex-like behaviors without specific physical media (that the phenomena arises in emergent fashion from behavioral rules), or as evidence that the observed behavior requires some specific set of physical parameters. [Preview Abstract] |
Monday, November 23, 2015 9:57AM - 10:10AM |
G23.00010: Numerical study of the hydrodynamic interactions in an \textit{E-coli} suspension Xinliang Xu The active suspension of \textit{E-coli} displays many interesting non-equilibrium phenomena, e.g. ``swarming'' at high bacteria concentrations, and viscosity change under simple shear. To understand the microscopic mechanism underlying these phenomena requires detailed knowledge about the hydrodynamics within the suspension. Here we numerically study in detail the hydrodynamic interactions between a bacterium and an ellipsoid tracer at small separations, where the tracer can no longer be treated as a point-like particle that creates no disturbance to local flow field. Based on Purcell's \textit{E-coli} model, we observed a significant drop in bacterium swimming velocity, in agreement with previous experimental study. [Preview Abstract] |
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