Polymer Translocation through a Nanopore: DPD Study

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Translocation of a polymer chain through a narrow pore is explored using 3D explicit solvent dissipative particle dynamics simulation. We study the dependence of the translocation dynamics and translocation time τ on the chain length N, driving force magnitude E, and solvent quality. Two types of driving forces are considered: uniform hydrostatic force, which is applied equally to the chain and solvent particles, and uniform electrostatic force, which is applied selectively to the charged particles in the chain and oppositely charged counterions in the solvent. We concluded that the scaling correlations τ ~ E(-ξ) and τ ~ N(β) are valid only for coil-like chains. For globular chains, the exponents ξ and β could not be identified with a reasonable accuracy. While the found value of ξ agrees with published experimental results and does not depend on the driving force type, the exponent β depends on the driving force and solvent quality. This is explained by nonequilibrium effects, as in the systems considered, the time of translocation is comparable with the time of chain relaxation. These effects, manifested in the changes of chain conformation in the process of translocation, were analyzed on the basis of the variation of the gyration radii of cis and trans segments of the chain in normal and lateral directions. A prominent chain expansion was observed for coils and was insignificant for globules. This work demonstrates the feasibility of the 3D dissipative particle dynamics modeling of translocation phenomena and accounting for the electrostatic interactions with explicit counterions, as well as for the solvent quality, in a computationally efficient manner.