Expansion dynamics of a self-avoiding polymer in a cylindrical pore

¹ National Institute of Supercomputing and Networking, Korea Institute of Science and Technology Information Daejeon 305-806, Korea
² Department of Physics and Astronomy, University of Waterloo - Waterloo, Ontario, Canada N2L 3G1
³ Department of Physics Education, Chosun University - Gwangju 501-759, Korea

^(a) yjung@kisti.re.kr
^(b) byha@uwaterloo.ca

Received: 7 October 2013
Accepted: 10 December 2013

Abstract

Inspired by recent bacterial chromosome experiments in narrow channels, we simulate the expansion (and internal) dynamics of a self-avoiding polymer under cylindrical confinement. The chain is trapped in a piston, compressed up to of its equilibrium length, and released unidirectionally from the right end of the piston. Our results suggest that the chain initially expands like a concentrated hard-sphere system, enters a subdiffusive regime at an intermediate time, and eventually relaxes globally to its equilibrium size. Using our results, we test a few theoretical models (e.g., a Flory-type approach), in which the blob-blob or monomer-monomer interaction determines “expansion forces,” clarifying their applicability. Our results can be used for exploring further the polymer aspect of bacterial chromosomes.