Paper Citing NAMD - Abstract
Lim, Melvin C. G.; Pei, Qx; Zhong, Z. W.
Translocation of DNA oligonucleotide through carbon nanotube channels under induced pressure difference
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 387:3111-3120, MAY 15 2008
This paper presents molecular dynamics (MD) simulations of DNA oligonucleotide and water molecules translocating through carbon nanotube (CNT) channels. Induced pressure difference is applied to the system by pushing a layer of water molecules towards the flow direction to drive the oligonucleotide and other molecules. This novel MD simulation investigates the flow behaviour of oligonucleotide and water molecules in nanochannel while controlling the temperature and volume of the system in canonical ensemble. The results show that the oligonucleotide is unable to translocate through the (8, 8)-(12, 12) CNT channel under the induced pressures applied. However, the oligonucleotide can transport through the (10, 10)-(14, 14) CNT channel easily under the same induced pressures. It is observed that less water molecules permeate through the center of the (8, 8)-(12, 12) CNT channel as the strength of the induced pressure is increased. In contrast, more water molecules flow through the (10, 10)-(14, 14) CNT channel at a higher induced pressure. The conformational energy of the oligonucleotide in the CNT channels has been shown to be affected by both the strength of the induced pressure and the size of the nanotube. Although the interactive force between oligonucleotide and CNT channel is dependent on their distance apart, the induced pressure within the (8, 8)-(12, 12) nanotube channel acts as an external factor that affects the distance between the oligonucleotide and the CNT junction. The insertion depth of the oligonucleotide, in the (8, 8)-(12, 12) CNT channel relies on the magnitude of the induced pressure. Both the velocity of oligonucleotide and the interactive force between oligonucleotide and nanotube wall are shown to increase when the oligonucleotide is travelling through the narrower part of the (10, 10)-(14, 14) CNT channel. (c) 2008 Elsevier B.V. All rights reserved.
