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:
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Chemical Physics Letters
- Pub Date:
- March 2020
- DOI:
- 10.1016/j.cplett.2020.137135
- Bibcode:
- 2020CPL...74237135I
- Keywords:
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- Self-assembly;
- Coarse-grained model;
- Molecular dynamics simulation