Polymer Translocation through a Nanopore: DPD Study

Abstract

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.

The design of shape-tunable hairy vesicles

“…Our measurements demonstrate the growth dynamics to slow down with concentration of the hairy lipids and the tether length. One possible explanation for the slower growth dynamics is the higher drag forces experienced by the lipid molecules due to the additional chain-like functional groups which have favorable enthalpic interactions with the solvent [35,36]. We find our results to be in good agreement with investigations on the aggregation dynamics of phospholipid molecules and hairy nanotubes [19].…”

“…The differences in the hydrocarbon tail groups such as the length is reflected in the transition temperature for the lipid molecules, and can be effectively captured by the tail-tail interaction parameter a t1t2 . The range of the tail-tail interaction parameter a t1t2 used in this investigation (31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48)(49)(50) has been demonstrated to promote macroscopic phase segregation in a binary phospholipid vesicle [31], and can model differences in the length of the hydrocarbon tails of the molecules. The simulations have been run for a time interval of 10,000 .…”

Modeling Aggregation of Ionic Surfactants Using a Smeared Charge Approximation in Dissipative Particle Dynamics Simulations

“…The smeared charge models have been applied to complex systems and phenomena, such as bulk electrolytes, individual polyelectrolyte molecules in electrolyte solutions, polymer brushes, polyelectrolyte translocation though narrow pores, hydrated polyelectrolyte membranes, peptides, and even dendrimer interactions with lipid bilayers. [13][14][17][18][19][20][21] Nevertheless, the predictive capabilities of the soft-core smeared charge models remain DPD studies of ionic surfactants using charge smearing have been quite limited. Very recently, Posel et al 17 tested the pH-dependent self-assembly of diblock copolymer using a Slatertype smearing charge distribution.…”

Suspended particle transport through constriction channel with Brownian motion

“…There are many situations where small objects subject to Brownian motion in a fluid are introduced to the constriction of microscopic channels, for example, filtration of colloidal particles through porous media [1][2][3], translocation of DNA molecules through nanopore sequencers [4][5][6][7][8][9][10][11][12][13][14][15][16][17], and lab-on-achip (LOC) devices where analytes are introduced to various domains of nano-and microchannels for analysis [18][19][20][21][22][23][24][25]. It is now well known that the translocation phenomena of polymer molecules through nanopores with a diameter comparable to the monomer size have stochastic nature [5,6].…”

“…Namely, the entropic barrier of Brownian objects into the constriction in these existing reports is caused by either a configuration within a chain structure or the orientation of an asymmetric shape. In this article, we report that even a simple point particle with perfect spherical symmetry without an inertial effect can exhibit the deviation of time-and 2470-0045/2017/96(2)/023109 (8) 023109-1 ©2017 American Physical Society ensemble-averaged dynamics from continuum flow field when translocated through the constriction part of the channel if the suspended particles are subject to significant Brownian motion.…”