ISSN Online: 2379-1748
ISBN Flash Drive: 978-1-56700-469-4
ISBN Online: 978-1-56700-470-0
Second Thermal and Fluids Engineering Conference
SIMULATION OF THE FLOW OF SINGLE STRANDED DNA THROUGH A MICROCHANNEL USING DISSIPATIVE PARTICLE DYNAMICS
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.