Coarse Grained Molecular Dynamics Simulations of Rod-Like Colloids and 3HB DNA nanostructures

Speaker: Jonathan Adams (MCSC)

Room: SHA 356

Abstract: We use Coarse Grained Molecular Dynamics to study two systems. The first is a system of rod-like colloids suspended in a solution of depletants. When a large number of small depeletent particles are in a solution with larger colloids, it is entropically favorable for the colloids to be clustered together. This causes an effective attractive force between the colloids, called the Depletion Force. We investigate using the depletion force to bundle rod-like colloids together. We also investigate the potential for selective bundling of rods based on length and stiffness.

The second system is of Triple Helix Bundles (3HB) translocating through a nanopore. The 3HB is a DNA origami structure, which is essentially 3 dsDNA strands stapled together. When driven through a nanopore by an electric field, we expect this structure to fold significantly less than dsDNA, due to its increased stiffness, but experiments conducted at uOttawa contradict this expectation. In collaboration with Vincent Tabard-Cossa’s experimental group at uOttawa, we propose defects in the 3HB as a possible cause of this discrepancy, and use MD simulations to study how the 3HB goes through a nanopore, both with and without defects.