A Polymer Spontaneously Ejecting from a Cavity to a Semi-Infinite Space through a Nanochannel

Pai-Yi Hsiao^1*

¹Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan

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

The remarkable problem of a polymer ejecting from a confining cavity into an outer semi-space through a nanochannel is investigated. A two-stage model is developed, in which an ejection process is divided into the confined and the non-confined stages. The ejection velocities in the two stages are derived with the help of the Onsager’s variational principle. The decrease of the number of the monomers in the cavity is therefore computed by solving the kinetics equations. The scaling properties of the ejection velocity and the ejection time are studied. The theory is then verified by means of molecular dynamics simulations. We vary the chain length and the cavity size such that the scaling behaviors are explored in the entire parameter spaces. An astonishing stalling behavior is observed at the beginning of a process. We are able to identify the stalling as a pre-stage related to the transportation of the heading monomers through the channel. We show that the pre-stage is analogous to a nucleation process and can be treated as a Kramers escape problem. After the pre-stage, the ejection process goes smoothly and can be properly described by the two-stage model. Physical pictures behind different ejection conditions are stated. The study provides deep insight into the complicated phenomena of biopolymer ejection occurred in nature and in applications.

Keywords: polymer ejection, scaling theory, molecular dynamics simulations