Cited Article: Hummer, G. Water conduction through the hydrophobic channel of a carbon nanotube
Alert Expires: 22 AUG 2011
Number of Citing Articles: 3 new records this week (3 in this e-mail)
Organization ID: 3b97d1bbc1878baed0ab183d8b03130b
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Title:
Aqua Ions-Graphene Interfacial and Confinement Behavior: Insights from Isobaric-Isothermal Molecular Dynamics
Authors:
Chialvo, AA; Cummings, PT
Author Full Names:
Chialvo, Ariel A.; Cummings, Peter T.
Source:
JOURNAL OF PHYSICAL CHEMISTRY A 115 (23): 5918-5927 JUN 16 2011
Language:
English
Document Type:
Article
KeyWords Plus:
HYDROGEN-BONDED STRUCTURE; AQUEOUS-SOLUTIONS; CARBON NANOTUBES; CONFIGURATIONAL TEMPERATURE; HYDRATION STRUCTURE; SURFACE POLARITY; LIQUID WATER; SIMULATION; POTENTIALS; GRAPHITE
Abstract:
We carry out a systematic microstructural characterization of the solid-fluid interface (SFI) of water and simple metal chloride aqueous solutions in contact with a freestanding plate or with two such plates separated by an interplate distance 0 <= h (angstrom) <= 30 at ambient conditions via isothermal-isobaric molecular dynamics. With this characterization, we target the interrogation of the system in search for answers to fundamental questions regarding the structure of the "external" and "internal" (confined) SFIs, the effect of the differential hydration behavior among species, and its link to species expulsion from confinement. For water at ambient conditions, we found that the structure of the "external" SFIs is independent of the interplate distance h in the range 0 <= h (angstrom) <= 30, that is, the absence of wall-mediated correlation effects between "external" and "internal" SFIs, and that for h < 9 angstrom the slit-pores dewet. Moreover, we observed a selective!
expulsion of ions caused by the differential hydration between the anion and the cations with a consequent charging of the slit-pore. All these observations were interpreted in terms of the axial profiles for precisely defined order parameters, including tetrahedral configuration, hydrogen bonding, and species coordination numbers.
Reprint Address:
Chialvo, AA, Oak Ridge Natl Lab, Chem Sci Div, Geochem & Interfacial Sci Grp, Oak Ridge, TN 37831 USA.
Research Institution addresses:
[Chialvo, Ariel A.] Oak Ridge Natl Lab, Chem Sci Div, Geochem & Interfacial Sci Grp, Oak Ridge, TN 37831 USA; [Cummings, Peter T.] Vanderbilt Univ, Dept Chem & Biomol Engn, Nashville, TN 37235 USA; [Cummings, Peter T.] Oak Ridge Natl Lab, Ctr Nanophase Mat Sci, Nanomat Theory Inst, Oak Ridge, TN 37831 USA
E-mail Address:
chialvoaa@ornl.gov
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Cited Reference Count:
70
Times Cited:
0
Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Subject Category:
Chemistry, Physical; Physics, Atomic, Molecular & Chemical
ISSN:
1089-5639
DOI:
10.1021/jp110318n
IDS Number:
773VG
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Title:
Modification of Martini force field for molecular dynamics simulation of hydrophobic charge induction chromatography of lysozyme
Authors:
Zhang, L; Bai, S; Sun, Y
Author Full Names:
Zhang, Lin; Bai, Shu; Sun, Yan
Source:
JOURNAL OF MOLECULAR GRAPHICS & MODELLING 29 (7): 906-914 JUN 2011
Language:
English
Document Type:
Article
Author Keywords:
Martini force field; Modification; Coarse-grained model; All-atom model; Protein adsorption; Desorption
KeyWords Plus:
EGG-WHITE LYSOZYME; COARSE-GRAINED MODEL; PROTEIN INSTABILITY; SOLID-SURFACE; ADSORPTION; PURIFICATION; ANTIBODIES; SEPARATION; FRAGMENTS; MECHANISM
Abstract:
Modeling, especially the force field, is crucial for the accuracy of molecular dynamics (MD) simulations. In order for more accurate description of adsorption and desorption behaviors of lysozyme in hydrophobic charge induction chromatography (HCIC), the Martini coarse-grained (CG) force field has been modified based on the statistical analysis and comparison of an all-atom (AA) force field, GROMOS96 43A1, and the Martini force field. The parameters describing the protein-adsorbent interactions have been adjusted to avoid too strong and unrealistic adsorption of lysozyme on the agarose matrix and HCIC ligands. It is found that the adsorption and desorption behaviors monitored using the modified Martini force field and MD simulation are consistent with previous simulation results with 46-bead beta-barrel model protein. Repeated adjustment of both protein position and orientation is necessary to generate enough contacts for a stable adsorption. After reducing the pH in the mob!
ile phase, the lysozyme-ligand electrostatic repulsion leads to protein desorption. In the adsorption process, little conformational transition of lysozyme is observed due to its stable structure, which is in line with previous experimental observations. So, it is concluded that after appropriate modification, the Martini force field can be used to examine the HCIC process of lysozyme. The modification strategy has thus extended the applicability of the Martini force field to protein chromatography, and it is expected to facilitate studies of exploring the molecular details in adsorption chromatography of proteins. (C) 2011 Elsevier Inc. All rights reserved.
Reprint Address:
Sun, Y, Tianjin Univ, Sch Chem Engn & Technol, Dept Biochem Engn, Tianjin 300072, Peoples R China.
Research Institution addresses:
[Sun, Yan] Tianjin Univ, Sch Chem Engn & Technol, Dept Biochem Engn, Tianjin 300072, Peoples R China; Tianjin Univ, Sch Chem Engn & Technol, Key Lab Syst Bioengn, Minist Educ, Tianjin 300072, Peoples R China
E-mail Address:
ysun@tju.edu.cn
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Cited Reference Count:
52
Times Cited:
0
Publisher:
ELSEVIER SCIENCE INC; 360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA
Subject Category:
Biochemical Research Methods; Biochemistry & Molecular Biology; Computer Science, Interdisciplinary Applications; Crystallography; Mathematical & Computational Biology
ISSN:
1093-3263
DOI:
10.1016/j.jmgm.2011.02.004
IDS Number:
774VL
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Title:
Interaction of Collagen with Carbon Nanotube: A Molecular Dynamics Investigation
Authors:
Gopalakrishnan, R; Subramanian, V
Author Full Names:
Gopalakrishnan, R.; Subramanian, V.
Source:
JOURNAL OF BIOMEDICAL NANOTECHNOLOGY 7 (1): 186-187 Sp. Iss. SI FEB 2011
Language:
English
Document Type:
Article
Author Keywords:
Carbon Nanotube (CNT); Collagen Like Peptides (CPs); Molecular Dynamics (MD) Simulation; Extra Cellular Matrix (ECM); Toxicity
Abstract:
In variety of biological applications carbon nano materials interact with different biological macromolecules, such as proteins, carbohydrates and nucleic acids. In this study carbon nanotube (CNT) has been used as the model for carbon nanomaterials. Since, collagen is a large protein; model collagen like peptide (CPs) has been used to understand the interaction between CNT and collagen. Molecular dynamics (MD) simulation showed that the hydrophobic hydrophobic interaction of the CNT-CPs play a crucial role in attracting the CPs towards the CNT. No structural aberrations occured in collagen upon interaction with CNT and hence CNT can be employed in the tissue engineering applications.
Reprint Address:
Gopalakrishnan, R, CSIR, Cent Leather Res Inst, Chem Lab, Madras 600020, Tamil Nadu, India.
Research Institution addresses:
[Gopalakrishnan, R.; Subramanian, V.] CSIR, Cent Leather Res Inst, Chem Lab, Madras 600020, Tamil Nadu, India
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Cited Reference Count:
9
Times Cited:
0
Publisher:
AMER SCIENTIFIC PUBLISHERS; 25650 NORTH LEWIS WAY, STEVENSON RANCH, CA 91381-1439 USA
Subject Category:
Nanoscience & Nanotechnology; Medicine, Research & Experimental
ISSN:
1550-7033
DOI:
10.1166/jbn.2011.1261
IDS Number:
774TZ
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