Public Library of Science
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Initial structure of four separated chains in a small space.

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journal contribution
posted on 2023-05-25, 17:45 authored by Gaurav Bajpai, Samuel Safran

The initial structure consists of four separate chains confined in a small space. By using moltemplate [85], one chain was generated, and then, by using packmol [103], four copies of chains were placed in a cubic box with a size of L = 100σ. The polymer system was then compressed to a small spherical confinement radius of Rc = 20σ (or ϕ = 0.6) using indented walls and Lennard-Jones (LJ) interactions. The force exerted by a spherical indenter on each bead is represented by the equation F(r) = −Kindent(rRindent)2, where Kindent is the specified force constant, r is the distance from the bead to the center of the indenter, and Rindent is the radius of the indenter [83]. The intra-chain interactions were attractive, with a strength of ϵintra = 1kBT and a cutoff distance of rc = 2.5σ, while the inter-chain interactions were repulsive, with a strength of ϵinter = 1kBT and a cutoff distance of rc = 21/6σ. A snapshot of the initial structure is shown in a confinement with a volume fraction of ϕ = 0.1, which illustrates that the chains were initially separated and condensed.