Modeling of Particle Interactions in DNA-laden Flows at the Microscale

We present a method for simulation of DNAladen flows in complex microscale geometries. In this method an incompressible Newtonian fluid is discretized with a finite difference method in the interior of the domain and a Cartesian grid embedded boundary/volume of fluid method is used near the boundary...

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Bibliographic Details
Published in:2006 International Conference of the IEEE Engineering in Medicine and Biology Society 2006, Vol.Supplement, p.6670-6673
Main Authors: Trebotichy, D., Millerz, G. H., Bybee, M. D.
Format: Article
Language:English
Subjects:
Biological system modeling
Cities and towns
Contracts
DNA
Geometry
Laboratories
Microfluidics
modeling
polymer flow
Polymers
Solid modeling
Solvents
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Summary:We present a method for simulation of DNAladen flows in complex microscale geometries. In this method an incompressible Newtonian fluid is discretized with a finite difference method in the interior of the domain and a Cartesian grid embedded boundary/volume of fluid method is used near the boundary. The DNA is represented by a bead-rod polymer model. The fluid and polymer are fully coupled through a body force representing hydrodynamic drag. The main objective in this work is to implement short range forces to properly model polymer-polymer and polymer-surface interactions. We will discuss two methods for these interactions: (1) a new rigid constraint algorithm whereby rods elastically bounce off one another, and (2) a classical (smooth) potential acting between rods. In addition, a smooth potential for the polymer-surface interactions is also implemented for comparison to the same interactions currently modeled by elastic collision.
ISSN:1557-170X
DOI:10.1109/IEMBS.2006.260917