Effects of Electrostatic Interactions on the Translocation of Polymers Through a Narrow Pore Under Different Solvent Conditions: A Dissipative Particle Dynamics Simulation Study

Abstract

The dynamics of polymer translocation through a narrow pore is significant in understanding several chemical and biological processes, such as the motion of DNA and RNA molecules across nanoscopic pores, infection of viruses into the cell nucleus, and transport of proteins through membrane channels. The translocation of polymer molecules through a narrow pore can also lead to several potentially industrial and technical applications, including rapid DNA sequencing, genomic partitioning techniques and information storage on macromolecules. It is not surprising that the translocation of polymers has become a subject of intensive experimental, [1][2][3][4][5][6][7] theoretical, [8][9][10][11][12][13][14][15][16] and computational studies [17][18][19][20][21][22][23] because its broad applications in many fields and its importance for understanding fundamental processes in biology and polymer sciences.The number of available configurations of polymers decreases during polymer translocation through a narrow pore, resulting in an effective entropic barrier for polymer molecules. Therefore, an external driving force, such as an external electric field, [1,4,18] a chemical potential gradi-Polymer translocation through a narrow pore is investigated using a particle-based dissipative particle dynamics (DPD) method. A rigid core is included in each particle to avoid particle interpenetration problems based on the original DPD method. Electrostatic interactions of charged particles are simply represented via screened Coulombic interactions. The average translocation time t versus polymer length N satisfies the scaling law t $ N b . The scaling exponent b depends on solvent quality. The results demonstrate that solvent quality exerts a considerable influence on the dynamics of translocation of polymers. The findings may help facilitate understanding of the dynamic behaviors of various polymer and DNA molecules during translocation processes.

Mesoscale simulations of two model systems in biophysics: from red blood cells to DNAs

“…5. The computational cost of calculating the continuum hydrody- [151,152], fast-multipole integration [153,154], and particlebased methods such as dissipative particle dynamics (DPD) [155,156], and multi-particle collision dynamics (MPCD) [85,157] have demonstrated O(N log (N )) efficiency for capturing long-range interactions such as hydrodynamics interaction. These developments have spurred new interests in the investigation of DNA dynamics in microfluidic flow and other systems.…”

“…They also com-pared the DPD simulation results with the experiments [186]. In order to consider explicitly the electrostatic interactions between particles and avoid the singularity caused by the Coulomb attraction between particles, hard-core interactions have often been employed to prevent [156,187]. For example, in addition to the typical DPD interactions shown in Eqs.…”

“…For example, in addition to the typical DPD interactions shown in Eqs. 4-6, Li et al used hard-core Morse interaction and a screened Coulombic interaction in the following form [156]:…”

“…It was also found that the translocation time predicted by LD is larger than that by DPD method. Li et al showed that the average translocation time τ scales with the polymer length N as τ ∼ N β [190], where β depends on the solvent quality [156] and could be adjusted by varying the repulsive parameter a P S between the polymer and the solvent in Eq. 4 as…”

“…The second challenge is the computational cost due to the long-range feature of the electrostatic interaction. A simple way to overcome these two challenges is to use a screened Coulombic interaction and another hard-core interaction to prevent overlap of the particles, as did in the work by Li et al [156], but significant error may be caused by these assumptions. A screened Coulombic interaction is employed as…”