Depletion induced bundling of rod-like colloids and simulations of triple helix bundles
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We ran molecular dynamics simulations of rod-like colloids acting under depletion forces. In these simulations, we found bundling of the rods above a given strength of the depletion force. We then analyzed the bundle formation process and how the shape and flexibility of the rods could effect bundle formation. We then looked at preferential bundling of long or stiff rods, and the hysteresis of bundle formation. We also collaborated with Vincent Tabard-Cossa’s lab at UOttawa to analyze the unexpected experimental behaviour of triple helix bundles folding through a nanopore. We ran coarse grained molecular dynamics simulations of 3HB to gain insight into the translocation process, and into the potential causes of the unexpected folding behaviour.