Coarse-grained modeling of nanocube self-assembly system and transition network analyses

Abstract An implicit-solvent coarse-grained (CG) model of a self-assembling molecular capsule called nanocube is developed based on all-atom molecular dynamics (MD) simulations and the iterative Boltzmann inversion method. The present model well describes the chemical specificity of constituent monomers (gear-shaped amphiphiles) and effective intermonomer interactions in aqueous methanol. Standard and replica exchange CG-MD simulations are performed and it is confirmed that the CG model can reproduce a highly ordered self-assembled structure similar to the AA model. Furthermore, the transition network is studied based on a cluster analysis, which suggests several major routes for the assembly via metastable bipyramidal states.

• Publication year

  2020

• Venue

  Chemical Physics Letters

• Publication date

  2020-03-01

• Fields of study

  Materials Science, Chemistry

• Identifiers
  DOI 10.1016/j.cplett.2020.137135
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

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