Paper Citing NAMD - Abstract
Xing, Yan-Fei; Yang, Chuan-Lu; Mo, Yong-Fang; Wang, Mei-Shan; Ma, Xiao-Guang
Dynamic Mechanism of Single-Stranded DNA Encapsulated into Single-Wall Carbon Nanotubes: A Molecular Dynamics Simulation Study
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 83 Art. No. 024801, FEB 2014
Hybrids of single-walled carbon nanotubes (SWCNTs) and biological molecules have been utilized for numerous applications in sensing, imaging, and drug delivery. By molecular dynamics simulation, we investigate the encapsulation of single-strand DNA (ssDNA) containing eight adenine bases with (17, 17)-(12, 12) SWCNTs. The effects of the diameter and length of SWCNTs on the encapsulation process are explored with the calculated curves of the center-of-mass distance, the van der Waals interaction between the ssDNA and SWCNT, the root-mean-square deviation of the ssDNA, and the radius of gyration of the ssDNA. The free energy of the encapsulated ssDNA for each SWCNT is also obtained via steered molecular dynamics simulation. The most suitable SWCNT for encapsulating the ssDNA is also suggested.
