Cited Article: Majumder M. Nanoscale hydrodynamics - Enhanced flow in carbon nanotubes
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Title:
Effects of fluid flow on the oligonucleotide folding in single-walled carbon nanotubes
Authors:
Lim, MCG; Zhong, ZW
Author Full Names:
Lim, M. C. G.; Zhong, Z. W.
Source:
PHYSICAL REVIEW E 80 (4): Art. No. 041915 Part 1 OCT 2009
Language:
English
Document Type:
Article
Author Keywords:
carbon nanotubes; DNA; high-pressure effects; molecular biophysics; molecular dynamics method; nanobiotechnology; van der Waals forces; water
KeyWords Plus:
MOLECULAR-DYNAMICS SIMULATION; SOLID-STATE NANOPORE; DNA TRANSLOCATION; LIQUID WATER; INSERTION; CHANNELS; TRANSPORT; DIAMETER
Abstract:
This paper presents molecular-dynamics (MD) simulations of DNA oligonucleotide and water molecules translocating through carbon nanotube (CNT) channels. An induced pressure difference is applied to the system by pushing a layer of water molecules toward the flow direction to drive the oligonucleotide and other molecules. This MD simulation investigates the changes that occur in the conformation of the oligonucleotide due to water molecules in nanochannels while controlling the temperature and volume of the system in a canonical ensemble. The results show that the oligonucleotide in the (8,8)-(12,12) CNT channel forms a folded state at a lower pressure, whereas the oligonucleotide in the (10,10)-(14,14) CNT channel forms a folded state at a higher pressure instead. The van der Waals forces between the water molecules and the oligonucleotide suggest that the attraction between these two types of molecules results in the linear arrangements of the bases of the oligonucleotide. !
For a larger nanotube channel, the folding of the oligonucleotide is mainly dependent on the solvent (water molecules), whereas pressure, the size of the nanotube junction, and water molecules are the considering factors of the folding of the oligonucleotide at a smaller nanotube channel. For a folded oligonucleotide, the water distribution around the oligonucleotide is concentrated at a smaller range than that for the distribution around an unfolded oligonucleotide.
Reprint Address:
Lim, MCG, Nanyang Technol Univ, Sch Mech & Aerosp Engn, 50 Nanyang Ave, Singapore 639798, Singapore.
Research Institution addresses:
[Lim, M. C. G.; Zhong, Z. W.] Nanyang Technol Univ, Sch Mech & Aerosp Engn, Singapore 639798, Singapore
Cited References:
ARAKI S, 2006, CHEM PHYS LETT, V418, P255, DOI 10.1016/j.cplett.2005.10.115.
BETHUNE DS, 1993, NATURE, V363, P605.
BONTHUIS DJ, 2008, PHYS REV LETT, V101, ARTN 108303.
FOLOGEA D, 2005, NANO LETT, V5, P1734, DOI 10.1021/nl051063o.
GAO HJ, 2003, NANO LETT, V3, P471, DOI 10.1021/nl025967a.
GAO HJ, 2004, ANNU REV MATER RES, V34, P123, DOI 10.1146/annurev.matsci.34.040203.120402.
GIGLIOTTI B, 2006, NANO LETT, V6, P159, DOI 10.1021/nl0518775.
HANASAKI I, 2006, MODEL SIMUL MATER SC, V14, S9, DOI 10.1088/0965-0393/14/5/S02.
HUMMER G, 2001, NATURE, V414, P188.
HUMPHREY W, 1996, J MOL GRAPHICS, V14, P33.
IIJIMA S, 1993, NATURE, V363, P603.
JOHNSON ATC, 2006, PHYS STATUS SOLIDI B, V243, P3252, DOI 10.1002/pssb.200669148.
JORGENSEN WL, 1983, J CHEM PHYS, V79, P926.
KATZ E, 2004, CHEMPHYSCHEM, V5, P1084.
LAU EY, 2005, CHEM PHYS LETT, V412, P82, DOI 10.1016/j.cplett.2005.05.129.
LI J, 1998, PHYS REV E, V57, P7259.
LIM MCG, 2008, PHYSICA A, V387, P3111, DOI 10.1016/j.physa.2008.01.111.
LIU GR, 2005, INT J MOD PHYS C, V16, P1239.
LIU Z, 2007, ANGEW CHEM INT EDIT, V46, P2023, DOI 10.1002/anie.200604295.
MACKERELL AD, 1998, J PHYS CHEM B, V102, P3586.
MAJUMDER M, 2005, NATURE, V438, P44, DOI 10.1038/43844a.
MUTHUKUMAR M, 1999, J CHEM PHYS, V111, P10371.
NAGUIB NN, 2005, NANOTECHNOLOGY, V16, P567, DOI 10.1088/0957-4484/16/4/038.
OKADA T, 2006, JPN J APPL PHYS 1, V45, P8335.
PHILLIPS JC, 2005, J COMPUT CHEM, V26, P1781.
PONNUSWAMY PK, 1994, J THEOR BIOL, V169, P419.
RATHORE N, 2006, BIOPHYS J, V90, P1767, DOI 10.1529/biophysj.105.071076.
SAITO R, 1996, PHYS REV B, V53, P2044.
SHI XH, 2005, ACTA MECH SINICA, V21, P249, DOI 10.1007/s10409-005-0027-9.
SINHA N, 2005, IEEE T NANOBIOSCI, V4, P180, DOI 10.1109/TNB.2005.850478.
STAR A, 2006, P NATL ACAD SCI USA, V103, P921.
STORM AJ, 2005, NANO LETT, V5, P1193, DOI 10.1021/nl048030d.
STRIOLO A, 2006, NANO LETT, V6, P633, DOI 10.1021/nl052254u.
SUN M, 1992, PHYS REV A, V46, P4813.
WAN RZ, 2005, J AM CHEM SOC, V127, P7166, DOI 10.1021/ja050044d.
WANG J, 2004, PHYS CHEM CHEM PHYS, V6, P829, DOI 10.1039/b313307a.
WEI C, 2005, INT J NANOSCI, V4, P363.
WONG KY, 2004, BIOPOLYMERS, V73, P570, DOI 10.1002/bip.20004.
XUE YQ, 2006, NANOTECHNOLOGY, V17, P5216, DOI 10.1088/0957-4484/17/20/029.
YEH IC, 2004, P NATL ACAD SCI USA, V101, P12177, DOI 10.1073/pnas.0402699101.
ZHANG C, 2008, J CHEM PHYS, V128, P25109, ARTN 225109.
ZHENG J, 2005, J CHEM PHYS, V122, P14702, ARTN 214702.
Cited Reference Count:
42
Times Cited:
0
Publisher:
AMER PHYSICAL SOC; ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA
Subject Category:
Physics, Fluids & Plasmas; Physics, Mathematical
ISSN:
1539-3755
DOI:
10.1103/PhysRevE.80.041915
IDS Number:
513UV
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