Ejection of a Polymer from a Cavity through a Small Pore to the Outer Space

Pai-Yi Hsiao^1*

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

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

We study the outstanding problem of a confined polymer being ejected from a spherical cavity into the outer semi-space through a short channel. A two-stage model is developed to understand the ejection process. We balance the free energy change with the energy dissipation and derive the ejection velocity in the two stages separately, namely, the confined stage and the non-confined stage. By solving the differential equations, the decreasing of the number of monomers in a cavity can be predicted and the ejection time is therefore obtained. The scaling behaviors of the ejection velocity and the ejection time are clearly described. The theory is then verified by performing extensive molecular dynamics simulations. We systematically vary the chain length and cavity diameter, and explore scaling behaviors over the entire parameter spaces. An astonishing stalling behavior in the progress of ejection is observed at the starting point. We are able to show that the stalling is a pre-stage for the head monomer to overcome the energy barrier in finding a way out of the channel. By varying the length of the pore, we prove that the pre-stage is, in fact, a nucleation stage which can be described by Kramers escape equation. After trimming the nucleation stage, the scaling behaviors of the ejection time can be properly studied. The results of simulation are found to support fully the predictions of the theory. The scaling of the nucleation time is also analyzed. Several physical pictures are given to explain polymer ejection under various conditions. (Funding number: MOST 109-2112-M-007-016.)

Keywords: polymer ejection, scaling theory, simulations