Coarse-grained molecular dynamics modeling of DNA–carbon nanotube complexes
Jian Zou
Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, U.S.A.
Search for more papers by this authorWentao Liang
Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, U.S.A.
Search for more papers by this authorCorresponding Author
Sulin Zhang
Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, U.S.A.
Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, U.S.A.Search for more papers by this authorJian Zou
Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, U.S.A.
Search for more papers by this authorWentao Liang
Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, U.S.A.
Search for more papers by this authorCorresponding Author
Sulin Zhang
Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, U.S.A.
Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, U.S.A.Search for more papers by this authorAbstract
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 © 2009 John Wiley & Sons, Ltd.
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