Library Subscription: Guest
Home Archives Officers Future meetings American Society of Thermal and Fluids Engineering
Second Thermal and Fluids Engineering  Conference

ISSN: 2379-1748
ISBN: 978-1-56700-430-4

SIMULATION OF THE FLOW OF SINGLE STRANDED DNA THROUGH A MICROCHANNEL USING DISSIPATIVE PARTICLE DYNAMICS

Saumya S. Simon
Oklahoma State University, Stillwater, OK 74078, USA

Khaled A. Sallam
School of Mechanical and Aerospace Engineering, Oklahoma State University, Tulsa, OK 74106, USA

Abstract

Dissipative Particle Dynamics (DPD) is used to simulate a system containing solvent and DNA strand as they migrate through a two-dimensional pressure-driven microchannel. DNA is modeled using worm-like chain. The physical characteristics of the movement of the DNA are investigated to understand the folding, coiling, tumbling and entanglements of the strand with varying external forces. The viscosity and particle interactions issue for standard DPD is corrected by modifying the weighing function of the dissipative and random force. This increases the viscosity of the DPD fluid particle to relate to the true fluid and keeps the computational cost to a minimum. The boundary conditions are altered to prevent the fluid particles from penetrating through the solid or 'frozen' wall particles. This reduces the need for multiple layering for the wall particle. The modifications have provided a valid Poiseuille's flow profile for a two-dimensional system. The results show that longer DNA strands appear to migrate towards the centerline for both standard DPD weighting functions and modified parameter. As longer strands entangle, strong internal forces are created which may cause more molecular deformation in a physical system.

Purchase $20.00 Check subscription Publication Ethics and Malpractice Recommend to my Librarian Bookmark this Page