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Synthesis of Cyclic Polymers and Characterization of Their Diffusive Motion in the Melt State at the Single Molecule Level

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Polymer translocation dynamics in the quasi-static limit.

James M Polson¹, Anthony C M McCaffrey

¹Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada.

The Journal of Chemical Physics

|May 10, 2013

Summary

Monte Carlo simulations reveal polymer translocation through nanopores in a quasi-static regime. Friction dominates, leading to translocation times scaling with polymer length, particularly in narrow pores.

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Area of Science:

Physics
Polymer Science
Computational Chemistry

Background:

Polymer translocation through nanopores is crucial for biological processes and nanotechnology.
Understanding translocation dynamics requires accurate modeling of polymer-nanopore interactions.
Previous studies often simplified the complex interplay of friction and polymer conformation.

Purpose of the Study:

To investigate polymer translocation dynamics in the quasi-static regime using Monte Carlo simulations.
To determine the scaling relationship between translocation time and polymer length.
To analyze the role of polymer-nanopore friction and free energy landscapes.

Main Methods:

Utilized Monte Carlo (MC) dynamics simulations to model a flexible hard-sphere polymer chain translocating through a cylindrical nanopore.
Employed a multiple-histogram method to compute free energy variations during translocation.
Applied the Fokker-Planck formalism, incorporating a friction coefficient (N(eff)), to derive theoretical translocation time distributions.

Main Results:

Established that for narrow pores, mean translocation time scales quadratically with polymer length (N) minus monomers in the pore (N(p)), indicating a quasi-static regime dominated by polymer-nanopore friction.
Demonstrated excellent quantitative agreement between theoretical and simulation-derived translocation time distributions for physically relevant effective monomer numbers (N(eff)).
Observed oscillations in free energy landscapes sensitive to nanopore length, correlating with translocation times.

Conclusions:

The quasi-static regime accurately describes polymer translocation in narrow nanopores, with friction being the dominant factor.
The developed theoretical framework, validated by MC simulations, provides a robust method for predicting translocation dynamics.
Nanopore geometry significantly influences free energy landscapes and, consequently, translocation times.