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

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 coarse-grained 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 single-stranded 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. Copyright (C) 2009 John Wiley & Sons, Ltd.