Paper Citing NAMD - Abstract
Chen, Bao-Dong; Yang, Chuan-Lu; Yang, Jun-Sheng; Wang, Mei-Shan; Ma, Xiao-Guang
The translocation of DNA oligonucleotide with the water stream in carbon nanotubes
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 991:93-97, JUL 1 2012
The translocation of biomolecule within carbon nanotubes (CNTs) has attracted great interest and has opened up exciting opportunities for drug delivery, gene detection and sequencing technology. To understand the fundamental interaction and the properties of translocation is indispensable but remains a challenge for both theoretical and experimental investigations. The present work focuses on the dynamics process of a single-stranded deoxyribonucleic acid (ssDNA) oligonucleotide through CNTs with a water-driven field using the steered molecular dynamics simulation. The van der Waals interaction and translocation time tau is used for analyzing the translocation process. The propulsion and obstruction forces for the movement of ssDNA are described. It is observed that both the strength of the water-driven field and the CNT channel size exert significant influence on the translocation process of ssDNA. Interestingly, both forces, the repulsive force from the water molecules behind ssDNA and the attractive interaction from water molecules in front of ssDNA, drive the ssDNA to move. The relationship between the translocation time and the water velocity is also examined. The present results can provide some helpful ideas for controlling biomolecule translocation process in CNT. (C) 2012 Elsevier B.V. All rights reserved.
