Incorporating surface polarization effects into large-scale coarse-grained Molecular Dynamics simulation

Trung Dac Nguyen, Honghao Li, Debarshee Bagchi, Francisco Solis, Monica Olvera de la Cruz

Research output: Contribution to journalArticle

Abstract

We implement and extend three methods for incorporating surface polarization effects into coarse-grained Molecular Dynamics (MD) simulations for LAMMPS: the boundary element method using the generalized minimum residual (GMRES) solver for solving the Poisson equation, the induced charge computation method using the successive over relaxations scheme, and the direct optimization of an energy functional of induced charge density. Our implementations are validated against the analytical results for several cases and against published results on electrolyte and polyelectrolyte adsorption on charged interfaces. We have also employed the mentioned methods to examine the effects of surface polarization due to dielectric mismatch on the conformational behavior and relaxation times of the Rouse modes of a highly charged polyelectrolyte with explicit multivalent counterions in a spherical droplet surrounded by a low dielectric medium. We have found that dielectric mismatch coupled with spatial confinement results in noticeable changes in the radius of gyration of the collapsed conformation as well as the work required to compress and stretch the chain. Dielectric confinement is therefore believed to play an important role in the packaging of polyelectrolytes, which was generally overlooked in previous studies. Finally, the parallel performance of the implemented methods for practical simulations is characterized for a model electrolyte system. For polarizable interfaces composed of more than 1000 mesh points, the induced charge computation method is found to be the most efficient.

Original languageEnglish (US)
JournalComputer Physics Communications
DOIs
StatePublished - Jan 1 2019

Fingerprint

Molecular dynamics
Polyelectrolytes
Polarization
molecular dynamics
Computer simulation
polarization
simulation
Electrolytes
electrolytes
gyration
Poisson equation
boundary element method
Boundary element method
Charge density
packaging
Relaxation time
Conformations
mesh
Packaging
relaxation time

Keywords

  • Coarse-grained Molecular Dynamics
  • Electrostatics
  • LAMMPS
  • Surface polarization

ASJC Scopus subject areas

  • Hardware and Architecture
  • Physics and Astronomy(all)

Cite this

Incorporating surface polarization effects into large-scale coarse-grained Molecular Dynamics simulation. / Nguyen, Trung Dac; Li, Honghao; Bagchi, Debarshee; Solis, Francisco; Olvera de la Cruz, Monica.

In: Computer Physics Communications, 01.01.2019.

Research output: Contribution to journalArticle

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