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Translocation of DNA oligonucleotide through carbon nanotube channels under induced pressure difference

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  • Lim, Melvin C.G.
  • Pei, Q.X.
  • Zhong, Z.W.

Abstract

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.

Suggested Citation

  • Lim, Melvin C.G. & Pei, Q.X. & Zhong, Z.W., 2008. "Translocation of DNA oligonucleotide through carbon nanotube channels under induced pressure difference," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 387(13), pages 3111-3120.
    • Handle: RePEc:eee:phsmap:v:387:y:2008:i:13:p:3111-3120
    DOI: 10.1016/j.physa.2008.01.111
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    References listed on IDEAS

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    1. G. Hummer & J. C. Rasaiah & J. P. Noworyta, 2001. "Water conduction through the hydrophobic channel of a carbon nanotube," Nature, Nature, vol. 414(6860), pages 188-190, November.
    2. Cheng, Y. & Liu, G.R. & Li, Z.R. & Lu, C., 2006. "Computational analysis of binding free energies between peptides and single-walled carbon nanotubes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 367(C), pages 293-304.
    3. G. R. Liu & Y. Cheng & Dong Mi & Z. R. Li, 2005. "A Study On Self-Insertion Of Peptides Into Single-Walled Carbon Nanotubes Based On Molecular Dynamics Simulation," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 16(08), pages 1239-1250.
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    Cited by:

    1. Lim, M.C.G. & Zhong, Z.W., 2009. "Molecular dynamics analyses of an Al(110) surface," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 388(19), pages 4083-4090.
    2. Lim, M.C.G. & Zhong, Z.W., 2011. "Effects of electromigration on copper atoms in carbon nanotube channels," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 390(5), pages 963-971.

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