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Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution

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Published on: August 16, 2016

Polymer translocation through a nanopore: DPD study.

Kan Yang¹, Aleksey Vishnyakov, Alexander V Neimark

¹Chemical and Biochemical Engineering, Rutgers University, 98 Brett Road, Piscataway, New Jersey 08854, USA.

The Journal of Physical Chemistry. B

|March 8, 2013

Summary

This summary is machine-generated.

Polymer translocation through pores is sensitive to chain shape and driving force. Dissipative particle dynamics reveals scaling laws depend on chain conformation and solvent quality, highlighting nonequilibrium effects.

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Area of Science:

Soft Matter Physics
Computational Biophysics
Polymer Science

Background:

Polymer translocation through nanopores is crucial for biological processes and nanotechnology.
Understanding translocation dynamics requires accurate simulation methods accounting for solvent and forces.

Purpose of the Study:

To investigate polymer translocation dynamics using 3D explicit solvent dissipative particle dynamics (DPD).
To analyze the influence of chain length, driving force, and solvent quality on translocation time.
To explore the impact of different driving forces (hydrostatic vs. electrostatic) on translocation.

Main Methods:

3D explicit solvent dissipative particle dynamics (DPD) simulations.
Systematic variation of polymer chain length (N), driving force magnitude (E), and solvent quality.
Analysis of translocation time (τ) and chain conformation using gyration radii.

Main Results:

Scaling correlations τ ~ E(-ξ) and τ ~ N(β) are valid for coil-like chains but not globular chains.
The exponent ξ is independent of driving force type, while β depends on driving force and solvent quality.
Nonequilibrium effects, indicated by chain expansion for coils, influence translocation dynamics.

Conclusions:

DPD is a computationally efficient method for modeling polymer translocation, including electrostatic interactions and solvent effects.
Chain conformation significantly impacts translocation dynamics and the validity of scaling laws.
Nonequilibrium effects are important when translocation time approaches chain relaxation time.