Coarse-grained molecular dynamics modeling of DNA-carbon nanotube complexes

Jian Zou, Wentao Liang, Sulin Zhang

Research output: Contribution to journalArticle

13 Scopus citations

Abstract

We present a coarse-grained method to study the energetics and morphologies of DNA-carbon nanotube (DNA-CNT) complexes in aqueous environment. In this method, we adopt an existing coarse-grained DNA model in which each nucleotide is coarse-grained by two interaction sites, one for the phosphate and sugar groups and the other for the base group. The interaction potentials between DNA sites and the carbon atoms on a CNT are parameterized through all-atom molecular dynamics (MD) simulations. The water molecules are treated implicitly using Langevin dynamics. The coarsegrained DNA-CNT model significantly improves the computational affordability, while captures the essential dynamics of DNA-CNT interactions observed from all-atom MD simulations. The coarse-grained method enables us to efficiently simulate adhesion, encapsulation, and wrapping processes of a singlestranded DNA molecule around CNTs. The simulation results agree with those obtained by all-atom MD simulations in several aspects. Our coarse-grained simulations provide useful guidelines in positioning DNA molecules on a CNT surface or graphene substrate in single-molecule experimental studies.

Original languageEnglish (US)
Pages (from-to)968-985
Number of pages18
JournalInternational Journal for Numerical Methods in Engineering
Volume83
Issue number8-9
DOIs
StatePublished - Aug 20 2010

All Science Journal Classification (ASJC) codes

  • Numerical Analysis
  • Engineering(all)
  • Applied Mathematics

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