Molecular Dynamics simulation of a polymer chain translocating through a nanoscopic pore |
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Authors: | M G Gauthier G W Slater |
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Institution: | (1) Department of Physics, University of Ottawa, 150 Louis-Pasteur, K1N 6N5 Ottawa, Ontario, Canada |
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Abstract: | The detection of linear polymers translocating through a nanoscopic pore is a promising idea for the development of new DNA
analysis techniques. However, the physics of constrained macromolecules and the fluid that surrounds them at the nanoscopic
scale is still not well understood. In fact, many theoretical models of polymer translocation neglect both excluded-volume
and hydrodynamic effects. We use Molecular Dynamics simulations with explicit solvent to study the impact of hydrodynamic
interactions on the translocation time of a polymer. The translocation time τ that we examine is the unbiased (no charge on
the chain and no driving force) escape time of a polymer that is initially placed halfway through a pore perforated in a monolayer
wall. In particular, we look at the effect of increasing the pore radius when only a small number of fluid particles can be
located in the pore as the polymer undergoes translocation, and we compare our results to the theoretical predictions of Chuang
et al. (Phys. Rev. E 65, 011802 (2001)). We observe that the scaling of the translocation time varies from τ ∼ N
11/5 to τ ∼ N
9/5 as the pore size increases (N is the number of monomers that goes up to 31 monomers). However, the scaling of the polymer relaxation time remains consistent
with the 9/5 power law for all pore radii. |
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Keywords: | 82 35 Lr Physical properties of polymers |
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