title: Modeling of particle interactions in DNA-laden flows at the microscale.
abstract: We present a method for simulation of DNA-laden 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.
authors.affiliation: Center for Applied Scientic Computing, Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551, USA.
authors.forename: D
authors.initials: D
authors.lastname: Trebotichy
authors.forename: G H
authors.initials: GH
authors.lastname: Millerz
authors.forename: M D
authors.initials: MD
authors.lastname: Bybee
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008956:Models, Chemical; D012212:Rheology
chemical_list: D004247:DNA