Expansion of Single Polymers Released from a Confined Cavity

Pai-Yi Hsiao^1,2*, Chia-Cheng Chu²

¹Department of Engineering and System Science, National Tsing Hua University, Hsinchu city, Taiwan
²Institute of Nuclear Engineering and Science, National Tsing Hua University, Hsinchu City, Taiwan

* Presenter:Pai-Yi Hsiao, email:pyhsiao@ess.nthu.edu.tw

In this work, we study the expansion of a polymer chain released from a confining cavity. The primary goal is to understand the kinetics of DNA or RNA chains released from a ruptured virus capsid, happened in infection of a cell. We first develop a two-stage model to explain the expansion phenomena. In the first stage, the chain expands by keeping a spherical shape while in the second stage, it expands like a coil. The kinetic equation of expansion is derived by using the Onsager’s variational principle. We then preform extensive molecular dynamics simulations to verify the theory. The simulations show supporting evidences for the theory. We are able to determine the characteristic time for the two expansion stages with good precision. The scaling behaviors of the characteristic time, the corresponding exponents, and the expansion velocities are studied in details. We discover that an expansion process is mainly dominated by the second stage. It allows us to propose a universal picture for the chain expansion, departed from an encapsulated state.

Keywords: polymer expansion, scaling theory, molecular dynamics simulations