Charged Polymers Confined in a Nanochannel Studied by Molecular Dynamics Simulations
Yu-Lin Lee1*, Pai-Yi Hsiao1
1Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan
* presenting author:Yu-Lin Lee,
When a single polymer is confined in a nano-scaled channel, the behaviors can be mainly divided into the two cases. In the first case, the channel’s diameter D is smaller than the persistence length P of the polymer. The chain is subject to a strong confinement and the condition is called the Odijk regime. In the second case, D is larger than P. The polymer is weakly confined in the channel. It is called the de Gennes regime. Although the confining behaviors in the two regimes have been intensively studied by computer simulations, the used models are mainly neutral polymers. The situation is quite different to the real experiments in which researchers are more interested in understanding confined biomolecules, such as DNA or proteins, in nanochannels for wide applications. These molecules are ionized in aqueous solutions and thus carry charges. Therefore, to understand correctly the system, one needs to study the problem with charged chains and ions. The ions can bring in the important screening and condensation effects, and makes the system not easy to be predicted. In this work, we perform molecular dynamics simulations to investigate charged polymers confined in a cylindrical channel. We use a coarse-grained method to model polyelectrolyte chains and ions in the solutions, and study the interaction between ions, polymers and channel wall. (This material is supported by Ministry of Science and Technology, under contract No. MOST 103-2112-M-007-014-MY3.)

Keywords: polymer confinement, biopolymer sequencing technology, polyelectrolyte