Cited Article: Hummer, G. Water conduction through the hydrophobic channel of a carbon nanotube
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Number of Citing Articles: 4 new records this week (4 in this e-mail)
Organization ID: 3b97d1bbc1878baed0ab183d8b03130b
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Title:
Molecular Transport through a Bottleneck Driven by External Force
Authors:
Nakajima, C; Hayakawa, H
Author Full Names:
Nakajima, Chihiro; Hayakawa, Hisao
Source:
PROGRESS OF THEORETICAL PHYSICS 122 (6): 1377-1390 DEC 2009
Language:
English
Document Type:
Article
KeyWords Plus:
DYNAMICS SIMULATION; FLOW; CONDUCTION; SYSTEMS; CHANNEL; MODEL
Abstract:
The transport phenomena of Lennard-Jones molecules through a structural bottleneck driven by all external force are investigated by molecular dynamics simulations. We observe two distinct molecular flow regimes distinguished by a critical external force F-c and find scaling behaviors between external forces and flow rates. Below the threshold F-c, molecules are essentially stuck in the bottleneck due to the attractive interaction between the molecules, while above F-c, molecules can smoothly move in the pipe. A critical flow rate q(c) corresponding to F-c satisfies a simple relationship with angles, and the value of q(c) can be estimated from a simple argument. We further clarify the role of the temperature dependence in the molecular flows through the bottleneck.
Reprint Address:
Nakajima, C, Kyoto Univ, Yukawa Inst Theoret Phys, Kyoto 6068502, Japan.
Research Institution addresses:
[Nakajima, Chihiro; Hayakawa, Hisao] Kyoto Univ, Yukawa Inst Theoret Phys, Kyoto 6068502, Japan
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Cited Reference Count:
40
Times Cited:
0
Publisher:
PROGRESS THEORETICAL PHYSICS PUBLICATION OFFICE; C/O KYOTO UNIV, YUKAWA HALL, KYOTO, 606-8502, JAPAN
Subject Category:
Physics, Multidisciplinary
ISSN:
0033-068X
IDS Number:
549YT
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Title:
Classical Density-Functional Theory of Inhomogeneous Water Including Explicit Molecular Structure and Nonlinear Dielectric Response
Authors:
Lischner, J; Arias, TA
Author Full Names:
Lischner, Johannes; Arias, T. A.
Source:
JOURNAL OF PHYSICAL CHEMISTRY B 114 (5): 1946-1953 FEB 11 2010
Language:
English
Document Type:
Article
KeyWords Plus:
NONUNIFORM POLYATOMIC SYSTEMS; FREEZING TRANSITION; ELECTRIC-FIELDS; LIQUID WATER; DYNAMICS; INTERFACE; SIMULATIONS; POTENTIALS; SOLVATION; FORCES
Abstract:
We present an accurate free-energy functional for liquid water written in terms of a set of effective potential fields in which fictitious noninteracting water molecules move. The functional contains an exact expression of the entropy of noninteracting molecules and thus provides an ideal starting point for the inclusion of complex intermolecular interactions which depend on the orientation of the interacting molecules. We show how an excess free-energy functional can be constructed to reproduce the following properties of water: the dielectric response; the experimental site-site correlation functions; the surface tension; the bulk modulus of the liquid and the variation of this modulus with pressure; the density of the liquid and the vapor phase; and liquid-vapor coexistence. As a demonstration, we present results for the application of this theory to the behavior of liquid water in a parallel plate capacitor. In particular, we make predictions for the dielectric response !
of water in the nonlinear regime, finding excellent agreement with known data.
Reprint Address:
Lischner, J, Cornell Univ, Atom & Solid State Phys Lab, Ithaca, NY 14853 USA.
Research Institution addresses:
[Lischner, Johannes; Arias, T. A.] Cornell Univ, Atom & Solid State Phys Lab, Ithaca, NY 14853 USA
E-mail Address:
jl597@cornell.edu
Cited References:
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Cited Reference Count:
51
Times Cited:
0
Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Subject Category:
Chemistry, Physical
ISSN:
1520-6106
DOI:
10.1021/jp9012224
IDS Number:
552EG
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Title:
Effects of Ligand Density on Hydrophobic Charge Induction Chromatography: Molecular Dynamics Simulation
Authors:
Zhang, L; Zhao, GF; Sun, Y
Author Full Names:
Zhang, Lin; Zhao, Guofeng; Sun, Yan
Source:
JOURNAL OF PHYSICAL CHEMISTRY B 114 (6): 2203-2211 FEB 18 2010
Language:
English
Document Type:
Article
KeyWords Plus:
PHASE LIQUID-CHROMATOGRAPHY; STATIONARY-PHASE; ADSORPTION MECHANISM; RETENTION MECHANISM; SURFACE COVERAGE; FOLDING KINETICS; BETA-HAIRPIN; CHAIN-LENGTH; PROTEIN-A; PURIFICATION
Abstract:
High ligand density is usually required in hydrophobic charge induction chromatography (HCIC) for high adsorption capacity. However, it is not clear to what extent the ligand density alters the adsorption and desorption behaviors, or if this leads to the protein conformational transition within adsorbent pores. In the present study, molecular dynamics simulation is performed to examine the effects of ligand density in HCIC using a 46-bead beta-barrel coarse-grained model protein and a coarse-grained adsorbent pore model established in our earlier work. Four ligand densities (1.474, 1.769, 2.212, and 2.949 mu mol/m(2)) are simulated at 298.15 K. The simulations indicate that both the capacity and irreversibility of adsorption increase with ligand density. However, it is found that the fastest adsorption occurs at a ligand density of 2.212 mu mol/m(2) rather than at the highest density studied. Analyses of adsorption trajectories, protein-ligand interaction energy, and the fre!
e energy map indicate that there is repulsion of protein when unfavorable contacts of the protein and ligands occur. There is an enhanced repulsion at 2.949 mu mol/m(2), which increases the energy barrier to the transition region and reduces the opportunities to get stable adsorption, thus leading to the decreased adsorption rate. At 2.212 mu mol/m(2), however, the repulsion is mild and the high ligand coverage provides abundant opportunities for the protein to get the fastest adsorption and thus causes the maximum unfolding. In the following simulations, complete and irreversible desorption is observed at all ligand densities, in agreement with the easy pH-induced elution behavior of HCIC observed experimentally. It is found that there is a suitable balance between hydrophobic attraction and electrostatic repulsion at 2.212 mu mol/m(2), which leads to the slowest desorption kinetics and causes the maximum unfolding. Moreover, analysis of unfolded protein distribution indic!
ates that unfolding occurs mainly on the ligand surface in bot!
h adsorp
tion and desorption. The behaviors have been comprehensively elucidated by molecular and thermodynamic analyses.
Reprint Address:
Sun, Y, Tianjin Univ, Dept Biochem Engn, Sch Chem Engn & Technol, Tianjin 300072, Peoples R China.
Research Institution addresses:
[Zhang, Lin; Zhao, Guofeng; Sun, Yan] Tianjin Univ, Dept Biochem Engn, Sch Chem Engn & Technol, Tianjin 300072, Peoples R China
E-mail Address:
ysun@tju.edu.cn
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55
Times Cited:
0
Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Subject Category:
Chemistry, Physical
ISSN:
1520-6106
DOI:
10.1021/jp903852c
IDS Number:
553GV
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Title:
Collective properties of water confined in carbon nanotubes: A computer simulation study
Authors:
Garberoglio, G
Author Full Names:
Garberoglio, G.
Source:
EUROPEAN PHYSICAL JOURNAL E 31 (1): 73-80 JAN 2010
Language:
English
Document Type:
Article
KeyWords Plus:
X-RAY-SCATTERING; LIQUID WATER; DYNAMICAL PROPERTIES; FAST SOUND; HYDROGEN STORAGE; LOW-FREQUENCY; BEHAVIOR; DIFFUSION; PHASE; MODE
Abstract:
The collective properties of water confined in the (10,10), (8,8) and (6,6) carbon nanotubes are studied by analysing the longitudinal-current autocorrelation function, calculated from computer-simulated trajectories. The corresponding spectra clearly show the presence of two excitations, but their behaviour is quite different from that observed in the case of bulk water. Instead of the strong positive dispersion of the hydrodynamic sound mode characteristic of bulk water (the fast-sound phenomenon), the sound dispersion relation of confined water is observed to flatten into a non-propagating mode, while a second excitation appears at a higher frequency. This behaviour is analysed in terms of the localized oscillation modes of the hydrogen-bond network.
Reprint Address:
Garberoglio, G, Univ Trent, CNISM, Via Sommarive 14, I-38100 Trento, Italy.
Research Institution addresses:
[Garberoglio, G.] Univ Trent, CNISM, I-38100 Trento, Italy; [Garberoglio, G.] Univ Trent, Dipartimento Fis, I-38100 Trento, Italy
E-mail Address:
garberog@science.unitn.it
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Cited Reference Count:
50
Times Cited:
0
Publisher:
SPRINGER; 233 SPRING ST, NEW YORK, NY 10013 USA
Subject Category:
Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Applied; Polymer Science
ISSN:
0253-2786
DOI:
10.1140/epje/i2010-10552-0
IDS Number:
553JG
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