NDLI: Modeling and Simulation of Hydrodynamic Interaction of DNA in a Micro-Fluidic Channel

Content Provider	The American Society of Mechanical Engineers (ASME) Digital Collection
Author	Raghavan, Sunitha Maahapatra, D. Roy Samanta, Arnab
Copyright Year	2013
Abstract	The motion of DNA (in the bulk solution) and the non-Newtonian effective fluid behavior are considered separately and self-consistently with the fluid motion satisfying the no-slip boundary condition on the surface of the confining geometry in the presence of channel pressure gradients. A different approach has been developed to model DNA in the micro-channel. In this study the DNA is assumed as an elastic chain with its characteristic Young’s modulus, Poisson’s ratio and density. The force which results from the fluid dynamic pressure, viscous forces and electromotive forces is applied to the elastic chain in a coupled manner. The velocity fields in the micro-channel are influenced by the transport properties. Simulations are carried out for the DNAs attached to the micro-fluidic wall. Numerical solutions based on a coupled multiphysics finite element scheme are presented. The modeling scheme is derived based on mass conservation including biomolecular mass, momentum balance including stress due to Coulomb force field and DNA-fluid interaction, and charge transport associated to DNA and other ionic complexes in the fluid. Variation in the velocity field for the non-Newtonian flow and the deformation of the DNA strand which results from the fluid-structure interaction are first studied considering a single DNA strand. Motion of the effective center of mass is analyzed considering various straight and coil geometries. Effects of DNA statistical parameters (geometry and spatial distribution of DNAs along the channel) on the effective flow behavior are analyzed. In particular, the dynamics of different DNA physical properties such as radius of gyration, end-to-end length etc. which are obtained from various different models (Kratky-Porod, Gaussian bead-spring etc.) are correlated to the nature of interaction and physical properties under the same background fluid environment.
Sponsorship	Nanotechnology Institute Bioengineering Division
File Format	PDF
ISBN	9780791845332
DOI	10.1115/NEMB2013-93127
Conference Proceedings	ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology
Language	English
Publisher Date	2013-02-04
Publisher Place	Boston, Massachusetts, USA
Access Restriction	Subscribed
Subject Keyword	Non-newtonian flow Chain Deformation Fluid structure interaction Pressure gradient Modeling Density Microchannels Young's modulus Fluids Center of mass Coulombs Springs Momentum Electromotive force Flow (dynamics) Pressure Stress Geometry Simulation Dynamics (mechanics) Poisson ratio Dna Boundary-value problems Finite element analysis Microfluidics
Content Type	Text
Resource Type	Article

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