Reduced-order molecular-dynamics model for polystyrene by equivalent-structure coarse graining

Abstract

This paper develops a reduced-order equivalent-structure based model for polystyrene in a rigid body molecular dynamics framework. In general, a coarse-grained model for polymers is obtained by replacing a group of chemically connected atoms by an effective particle and deriving a coarse-grained interaction potential that reproduces the structure and dynamics at the desired length and time scale. In the current model, a detailed (~16 atoms) polystyrene monomer referred to as basic structural element (BSE) is replaced by an equivalent model with spherical backbone particles and an ellipsoidal particle that represents the styrene sidegroup. The governing principals of this homogenization is based on the mass, centroid, angular momentum, and energy equivalence between the detailed and the proposed reduced-order model. The bonded interactions parameters are readily obtained in the optimization of the equivalent structure from the detailed representation. The nonbonded interactions are treated separately. In order to capture the stereochemistry of the polystyrene molecule, an anisotropic biaxial nonbonded interaction potential function known as RE-squared (RE2) interaction has been used between pairs of ellipsoidal and/or spherical particles in the system. The required calibration of the nonbonded parameters is carried out by matching with the experimental density and the local structure using radial distribution function. This homogenization process scales up the modeling system size significantly as the higher frequency motions like -C-H- vibrations and sidegroup movements are suppressed. The accuracy of the model is established by comparing fine-scale simulation with explicit representations.

Coarse-Grained Molecular Dynamics Study of the Curing and Properties of Highly Cross-Linked Epoxy Polymers

“…Instead, simplified potential fields are often used, , which poorly simulate the conformation of chains in the network. In the second technique, the focus is on matching the structural aspects of the material, such as the centroid, mass, and angular momentum, through adjusting the mean forces derived from the Boltzmann inversion − or inverse Monte Carlo methods . The coarse-grained potential fields developed in this technique must be used for simulations having identical thermodynamic conditions to those they were fitted to .…”

Assessment of an anisotropic coarse-grained model for cis-1,4-polybutadiene: a bottom-up approach

“…As done in the Gay-Berne potential 41,42 , we could assume that the anisotropic potential also depends on the angles φµ and φν defined as cos φµ = u µ,1 • eµν and cos φν = −u ν,1 • eµν . This has been done in different coarse-grained anisotropic potentials designed over the years [23][24][25]48,49 . This assumption, changes the orientation of the force, which now have contributions along ∂ cos φµ/∂Rµ and ∂ cos φν /∂Rµ, and not only along eµν .…”

“…The anisotropy of the bead in particular is an obvious complementary coarse-grained variable when beads are clearly anisotropic, like ellipsoidal colloids [17][18][19][20] . Anisotropic CG potentials have been derived in a bottom-up approach for example for amino acids in proteins 21,22 and for monomers in polystyrene 23,24 or semiflexible ring polymers 25,26 . In these studies, the improvement of the structural properties of the CG system when the anisotropy is taken into account has been tested by using CG Monte-Carlo simulations.…”