Role of non-equilibrium conformations on driven polymer translocation

Area of Science:

• Polymer Physics
• Soft Matter Physics
• Computational Biophysics

Background:

• The Fokker-Planck formalism is a key theoretical tool for polymer translocation, relying on a quasi-equilibrium assumption.
• The validity of this approximation depends on the translocation time per Kuhn segment being longer than the polymer's relaxation time.

Purpose of the Study:

• To investigate the conditions under which the quasi-equilibrium approximation is applicable for polymer translocation.
• To study the influence of initial polymer conformations on translocation kinetics.
• To compare simulation results with theoretical predictions and experimental data.

Main Methods:

• Coarse-grained three-dimensional Langevin dynamics simulations.
• Multi-particle collision dynamics simulations.
• Systematic generation of stretched (out-of-equilibrium) initial polyelectrolyte chain conformations.
• Independent simulations to determine polymer relaxation times.

Main Results:

• Artificially stretched initial states violate the quasi-equilibrium criterion (⟨τ⟩/N_K < τ₀).
• Despite violating the criterion, translocation time scales as ⟨τ⟩ ∼ 1/V, consistent with Fokker-Planck predictions.
• For realistic, non-flow conditions, experimental data suggest non-equilibrium dynamics (⟨τ⟩/N_K < τ_Zimm) for flexible polymers like ssDNA.

Conclusions:

• The quasi-equilibrium approximation is not always applicable for polymer translocation, particularly with non-equilibrium initial states.
• A crossover from quasi-equilibrium to non-equilibrium behavior is predicted for flexible polymers around N_K ∼ O(1000).
• Understanding non-equilibrium dynamics is essential for accurate modeling of polymer translocation across nanopores.