Theoretical model of biomacromolecule through nanopore including effects of electrolyte and excluded volume

Abstract

A theoretical model for the translocation process of biomacromolecule is developed based on the self-consistent field theory (SCFT), where the biomacromolecule is regarded as a self-avoiding polymer chain actuated by the external potential. In this theoretical model, the external potential, the Coulomb electrostatic potential of the charged ions (the electrolyte effect), and the attractive interaction between the polymer and the nanopore (the excluded volume effect) are all considered, which have effects on the free energy landscape and conformation entropy during the translocation stage. The result shows that the entropy barrier of the polymer in the solution with high valence electrolyte is much larger than that with low valence electrolyte under the same condition, leading to that the translocation time of the DNA molecules in the solution increases when the valence electrolyte increases. In addition, the attractive interaction between the polymer and the nanopore increases the free energy of the polymer, which means that the probability of the translocation through the nanopore increases. The average translocation time decreases when the excluded volume effect parameter increases. The electrolyte effect can prolong the average translocation time. The simulation results agree well with the available experimental results.