Three-dimensional kinetic simulations of active suspensions: effect of chemotaxis and steric interaction

Ezhilan, Barath

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https://hdl.handle.net/2142/29521 Copy

Description

Title

Three-dimensional kinetic simulations of active suspensions: effect of chemotaxis and steric interaction

Author(s)

Ezhilan, Barath

Issue Date

2012-02-01T00:53:50Z

Director of Research (if dissertation) or Advisor (if thesis)

Saintillan, David

Department of Study

Mechanical Sci & Engineering

Discipline

Mechanical Engineering

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

M.S.

Degree Level

Thesis

Keyword(s)

• active suspensions
• concentrated
• self-propelled
• nematic
• Bacteria
• swimming
• oxygentaxis
• chemotaxis
• steric
• kinetic model
• low reynolds number
• Active Matter
• living fluids
• three-dimensional
• Numerical simulation
• number density fluctuation
• Instabilities

Abstract

In this work, the effects of chemotaxis and steric interactions in active suspensions are analyzed by extending the kinetic model proposed by Saintillan and Shelley [1, 2]. In this model, a conservation equation for the active particle configuration is coupled to the Stokes equation for the flow arising from the force dipole exerted by the particles on the fluid. The fluid flow equations are solved spectrally and the conservation equation is solved by second-order finite differencing in space and second-order Adams-Bashforth time marching. First, the dynamics in suspensions of oxytactic run-and-tumble bacteria confined in thin liquid films surrounded by air is investigated. These bacteria modify their tumbling behavior by making temporal comparisons of the oxygen concentration, and, on average, swim towards high concentrations of oxygen. The kinetic model proposed by Saintillan and Shelley [1, 2] is modified to include run-and-tumble effects and oxygentaxis. The spatio-temporal dynamics of the oxygen and bacterial concentration are analyzed. For small film thicknesses, there is a weak migration of bacteria to the boundaries, and the oxygen concentration is high inside the film as a result of diffusion; both bacterial and oxygen concentrations quickly reach steady states. Above a critical film thickness (approximately 200 micron), a transition to chaotic dynamics is observed and is characterized by turbulent-like 3D motion, the formation of bacterial plumes, enhanced oxygen mixing and transport into the film, and hydrodynamic velocities of magnitudes up to 7 times the single bacterial swimming speed. The simulations demonstrate that the combined effects of hydrodynamic interactions and oxygentaxis create collective three-dimensional instabilities which enhances oxygen availability for the bacteria. Our simulation results are consistent with the experimental findings of Sokolov et al. [3], who also observed a similar transition with increasing film thickness. Next, the dynamics in concentrated suspensions of active self-propelled particles in a 3D periodic domain are analyzed. We modify the kinetic model of Saintillan and Shelley [1, 2] by including an additional nematic alignment torque proportional to the local concentration in the equation for the rotational velocity of the particles, causing them to align locally with their neighbors (Doi and Edwards [4]). Large-scale three- dimensional simulations show that, in the presence of such a torque both pusher and puller suspensions are unstable to random fluctuations and are characterized by highly nematic structures. Detailed measures are defined to quantify the degree and direction of alignment, and the effects of steric interactions on pattern formation will be presented. Our analysis shows that steric interactions have a destabilizing effect in active suspensions.

Graduation Semester

2011-12

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http://hdl.handle.net/2142/29521

Copyright and License Information

2011 by Barath Ezhilan. All rights reserved.

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