Dynamics of single semiflexible filaments in a viscous fluid

Manikantan, Harishankar

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https://hdl.handle.net/2142/32000 Copy

Description

Title

Dynamics of single semiflexible filaments in a viscous fluid

Author(s)

Manikantan, Harishankar

Issue Date

2012-06-27T21:23:54Z

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

Saintillan, David

Department of Study

Mechanical Sci & Engineering

Discipline

Theoretical & Applied Mechans

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

M.S.

Degree Level

Thesis

Keyword(s)

• biophysical fluid dynamics
• slender body theory
• semiflexible polymer
• filament
• Stokes flow
• buckling instability
• elasticity
• Brownian force
• numerical simulation

Abstract

Numerous cellular functions rely on semiflexible filaments as structural elements (F-actin, microtubules), locomotive organs (flagella, cilia) or carriers of information (DNA). Flexible and semiflexible polymers are also commonly encountered in technological applications, specifically in chemical engineering and materials sciences. A thorough description of the physics involved can be achieved only through a detailed modeling and understanding of their mechanical properties and dynamics. With recent advances in nanofabrication techniques and experimental capabilities using microfluidic devices, there has been a renewed interest in the dynamics of semiflexible polymers. In this work, we present a detailed and efficient simulation method for solutions of short single semiflexible polymers using slender body theory in Stokes flow. An algorithm is developed that takes into account the inextensibility and elasticity of the filament, and accounts for hydrodynamic as well as Brownian forces. This is tested against theoretically known and experimentally verified equilibrium properties and scaling laws. We then focus on flow fields commonly observed in microfluidic devices, particularly the dynamics of bio-polymers in linear shear flows and near hyperbolic stagnation points. In linear shear flow, Brownian fluctuations dislodge the filament from an otherwise stable axis resulting in a characteristic tumbling motion. A sub-linear growth of tumbling frequency with shear rate is obtained that matches with experimental observations. Also, interesting non-linear behavior of the filament shape is observed in the case of hyperbolic flow geometries that are prevalent in microfluidic devices used to separate, observe and manipulate single macromolecules. Thermal fluctuations are suppressed by the flow when the filament is aligned with the extensional axis, and this suppression is shown to depend on the rate of extension of the external flow. Similarly, in the compressional regime, filaments undergo a buckling instability similar to Euler buckling of beams, taking on higher mode shapes with increasing flow strengths. Both suppression and buckling are attributed to a competition between tension and elasticity. Our study confirms the existence of this stretch-coil transition, which could also explain certain biophysical aspects of filament rearrangement in streaming and bio-locomotion. A detailed characterization of such behavior pertaining specifically to flow fields commonly seen in microfluidic devices will aid in the design of such devices constructed particularly for trapping, separating and precise control of single polymer molecules. Furthermore, the model developed here can be potentially extended to include interactions and electrokinetic phenomena that may then lead to solving problems in applications like DNA electrophoresis and polymer translocation through pores.

Graduation Semester

2012-05

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http://hdl.handle.net/2142/32000

Copyright and License Information

Copyright 2012 by Harishankar Manikantan. All rights reserved.

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