Kinetics of the ejection of a polymer from a capsid : a molecular dynamics approach -

Abstract

In this thesis we investigate the problem of a polymer chain ejecting from a cylindrically symmetric capsid. We approach the problem through molecular dynamics simulations using a bead spring model for the chain, and a strongly repulsive potential for the walls of the capsid. We formulate two theories to get predictions for the ejection times, one deterministic and one stochastic. We also introduce a method to calculate local pressure distribution in cylindrical coordinates. The simulation results show some deviations from the theory which is an indication that we need to improve the theoretical model.