Cited Article: Hummer, G. Water conduction through the hydrophobic channel of a carbon nanotube
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Title:
Water-mediated signal multiplication with Y-shaped carbon nanotubes
Authors:
Tu, YS; Xiu, P; Wan, RZ; Hu, J; Zhou, RH; Fang, HP
Author Full Names:
Tu, Yusong; Xiu, Peng; Wan, Rongzheng; Hu, Jun; Zhou, Ruhong; Fang, Haiping
Source:
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 106 (43): 18120-18124 OCT 27 2009
Language:
English
Document Type:
Article
Author Keywords:
confined water; molecular dynamics; molecular signal transmission; Y-shaped nanochannel; signal transduction
KeyWords Plus:
MOLECULAR-DYNAMICS; CHANNEL; MECHANISM; TRANSPORT; CONDUCTION; JUNCTIONS; ELECTRON; LOGIC; FLOW
Abstract:
Molecular scale signal conversion and multiplication is of particular importance in many physical and biological applications, such as molecular switches, nano-gates, biosensors, and various neural systems. Unfortunately, little is currently known regarding the signal processing at the molecular level, partly due to the significant noises arising from the thermal fluctuations and interferences between branch signals. Here, we use molecular dynamics simulations to show that a signal at the single-electron level can be converted and multiplied into 2 or more signals by water chains confined in a narrow Y-shaped nanochannel. This remarkable transduction capability of molecular signal by Y-shaped nanochannel is found to be attributable to the surprisingly strong dipole-induced ordering of such water chains, such that the concerted water orientations in the 2 branches of the Y-shaped nanotubes can be modulated by the water orientation in the main channel. The response to the swit!
ching of the charge signal is very rapid, from a few nanoseconds to a few hundred nanoseconds. Furthermore, simulations with various water models, including TIP3P, TIP4P, and SPC/E, show that the transduction capability of the Y-shaped carbon nanotubes is very robust at room temperature, with the interference between branch signals negligible.
Reprint Address:
Zhou, RH, IBM Thomas J Watson Res Ctr, Yorktown Hts, NY 10598 USA.
Research Institution addresses:
[Zhou, Ruhong] IBM Thomas J Watson Res Ctr, Yorktown Hts, NY 10598 USA; [Tu, Yusong; Xiu, Peng; Wan, Rongzheng; Hu, Jun; Fang, Haiping] Chinese Acad Sci, Shanghai Inst Appl Phys, Shanghai 201800, Peoples R China; [Tu, Yusong] Chinese Acad Sci, Grad Sch, Beijing 100080, Peoples R China; [Xiu, Peng] Shandong Univ, Sch Phys, Jinan 250100, Peoples R China; [Zhou, Ruhong] Columbia Univ, Dept Chem, New York, NY 10027 USA
E-mail Address:
ruhongz@us.ibm.com; fanghaiping@sinap.ac.cn
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Cited Reference Count:
42
Times Cited:
0
Publisher:
NATL ACAD SCIENCES; 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA
Subject Category:
Multidisciplinary Sciences
ISSN:
0027-8424
DOI:
10.1073/pnas.0902676106
IDS Number:
512DB
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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
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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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Title:
Characterization of Water Wires inside Hydrophobic Tubular Peptide Structures
Authors:
Raghavender, US; Aravinda, S; Shamala, N; Kantharaju; Rai, R; Balaram, P
Author Full Names:
Raghavender, Upadhyayula S.; Aravinda, Subrayashastry; Shamala, Narayanaswamy; Kantharaju; Rai, Rajkishor; Balaram, Padmanabhan
Source:
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 131 (42): 15130-+ OCT 28 2009
Language:
English
Document Type:
Article
KeyWords Plus:
CARBON NANOTUBES; CHANNELS; DYNAMICS
Abstract:
The crystallographic observation of a hydrophobic, empty channel (diameter similar to 5.2 angstrom) in the peptide Boc-(D)Pro-Aib-Leu-Aib-Val-OMe, prompted the investigation of the analog Boc-(D)Pro-Aib-Val-Aib-Val-OMe in which the side chain at position 3 was shortened, resulting in the structure of a channel (diameter similar to 7.5 angstrom) containing a one-dimensional wire of water molecules. Crystallization in the space group P6(5) facilitates formation of a pore tined entirety by hydrocarbon side chains. Two forms of the entrapped water wires, with O center dot center dot center dot O separations of 3.5 and 2.6 angstrom, are discussed. A lone hydrogen bond between the adjacent pairs of water molecules in the wire, with no strong interactions between the second water hydrogen and the hydrophobic walls of the channel, is a feature of the one-dimensional array. The structure provides the first crystallographic characterization of a water wire in a hydrophobic channel wit!
h implications in water and proton transport in membranes and carbon nanotubes
Reprint Address:
Shamala, N, Indian Inst Sci, Dept Phys, Bangalore 560012, Karnataka, India.
Research Institution addresses:
[Raghavender, Upadhyayula S.; Aravinda, Subrayashastry; Shamala, Narayanaswamy] Indian Inst Sci, Dept Phys, Bangalore 560012, Karnataka, India; [Kantharaju; Rai, Rajkishor; Balaram, Padmanabhan] Indian Inst Sci, Mol Biophys Unit, Bangalore 560012, Karnataka, India
E-mail Address:
shamala@physics.iisc.ernet.in; pb@mbu.iisc.ernet.in
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Cited Reference Count:
23
Times Cited:
0
Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Subject Category:
Chemistry, Multidisciplinary
ISSN:
0002-7863
DOI:
10.1021/ja9038906
IDS Number:
512SX
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