Citation Alerts

Friday, January 28, 2011

ISI Web of Knowledge Alert - Hummer, G

ISI Web of Knowledge Citation Alert

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:
Tribological Effects on DNA Translocation in a Nanochannel Coated with a Self-Assembled Monolayer

Authors:
Luan, BQ; Afzali, A; Harrer, S; Peng, HB; Waggoner, P; Polonsky, S; Stolovitzky, G; Martyna, G

Author Full Names:
Luan, Binquan; Afzali, Ali; Harrer, Stefan; Peng, Hongbo; Waggoner, Philip; Polonsky, Stas; Stolovitzky, Gustavo; Martyna, Glenn

Source:
JOURNAL OF PHYSICAL CHEMISTRY B 114 (51): 17172-17176 DEC 30 2010

Language:
English

Document Type:
Article

KeyWords Plus:
MOLECULE MASS-SPECTROMETRY; SOLID-STATE NANOPORE; TRANSPORT; CHANNELS; DYNAMICS; WATER; PROTEINS; FRICTION; PORE

Abstract:
A biomimetic nanochannel coated with a self-assembled monolayer (SAM) can be used for sensing and analyzing biomolecules. The interaction between a transported biomolecule and a SAM governs the mechanically or electrically driven motion of the molecule. To investigate the translocation dynamics of a biomolecule, we performed all-atom molecular dynamics simulations on a single-stranded DNA in a solid-state nanochannel coated with a SAM that consists of octane or octanol polymers. Simulation results demonstrate that the interaction between DNA and a hydrophobic or a hydrophilic SAM is effectively repulsive or adhesive, respectively, resulting in different translocation dynamics of DNA. Therefore, with proper designs of SAMs coated on a channel surface, it is possible to control the translocation dynamics of a biomolecule. This work also demonstrates that traditional tribology methods can be deployed to study a biological, or biomimetic transport process.

Reprint Address:
Luan, BQ, IBM Corp, Thomas J Watson Res Ctr, 1101 Kitchawan Rd, Yorktown Hts, NY 10598 USA.

Research Institution addresses:
[Luan, Binquan; Afzali, Ali; Harrer, Stefan; Peng, Hongbo; Waggoner, Philip; Polonsky, Stas; Stolovitzky, Gustavo; Martyna, Glenn] IBM Corp, Thomas J Watson Res Ctr, Yorktown Hts, NY 10598 USA

E-mail Address:
bluan@us.ibm.com

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Cited Reference Count:
29

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/jp108865q

IDS Number:
697ZN

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Title:
Structure and adsorption of water in nonuniform cylindrical nanopores

Authors:
Torrie, GM; Lakatos, G; Patey, GN

Author Full Names:
Torrie, G. M.; Lakatos, G.; Patey, G. N.

Source:
JOURNAL OF CHEMICAL PHYSICS 133 (22): Art. No. 224703 DEC 14 2010

Language:
English

Document Type:
Article

KeyWords Plus:
CARBON NANOTUBES; MOLECULAR-DYNAMICS; ICE NANOTUBES; K+ CHANNEL; POTENTIALS; CONDUCTION; IONS

Abstract:
Grand canonical Monte Carlo simulations are used to examine the adsorption and structure of water in the interior of cylindrical nanopores in which the axial symmetry is broken either by varying the radius as a function of position along the pore axis or by introducing regions where the characteristic strength of the water-nanopore interaction is reduced. Using the extended simple point charge (SPC/E) model for water, nanopores with a uniform radius of 6.0 angstrom are found to fill with water at chemical potentials approximately 0.5 kJ/mol higher than the chemical potential of the saturated vapor. The water in these filled pores exists in either a weakly structured fluidlike state or a highly structured uniformly polarized state composed of a series of stacked water clusters with pentagonal cross sections. This highly structured state can be disrupted by creating hydrophobic regions on the surface of the nanopore, and the degree of disruption can be systematically controlled
by adjusting the size of the hydrophobic regions. In particular, hydrophobic banded regions with lengths larger than 9.2 angstrom result in a complete loss of structure and the formation of a liquid-vapor coexistence in the tube interior. Similarly, the introduction of spatial variation in the nanopore radius can produce two condensation transitions at distinct points along the filling isotherm. (C) 2010 American Institute of Physics. [doi:10.1063/1.3505453]

Reprint Address:
Patey, GN, Univ British Columbia, Dept Chem, Vancouver, BC, Canada.

Research Institution addresses:
[Lakatos, G.; Patey, G. N.] Univ British Columbia, Dept Chem, Vancouver, BC, Canada; [Torrie, G. M.] Royal Mil Coll Canada, Dept Chem & Chem Engn, Kingston, ON, Canada

E-mail Address:
torrie-g@rmc.ca; glakatos@chem.ubc.ca; patey@chem.ubc.ca

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Cited Reference Count:
28

Times Cited:
0

Publisher:
AMER INST PHYSICS; CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA

Subject Category:
Physics, Atomic, Molecular & Chemical

ISSN:
0021-9606

DOI:
10.1063/1.3505453

IDS Number:
696YR

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Title:
Plugging into Proteins: Poisoning Protein Function by a Hydrophobic Nanoparticle

Authors:
Zuo, GH; Huang, Q; Wei, GH; Zhou, RH; Fang, HP

Author Full Names:
Zuo, Guanghong; Huang, Qing; Wei, Guanghong; Zhou, Ruhong; Fang, Haiping

Source:
ACS NANO 4 (12): 7508-7514 DEC 2010

Language:
English

Document Type:
Article

Author Keywords:
nanoparticle toxicity; protein-nanoparticle interaction; protein function poisoning; hydrophobic interaction; molecular dynamics

KeyWords Plus:
WALLED-CARBON-NANOTUBES; REPLICA EXCHANGE; MULTIDOMAIN PROTEIN; IN-VIVO; MICE; SIMULATION; DYNAMICS; CHANNEL; NANOTECHNOLOGY; RECOGNITION

Abstract:
Nanoscale particles have become promising materials In many fields, such as cancer therapeutics, diagnosis, Imaging, drug delivery, catalysis, as well as biosensors. In order to stimulate and facilitate these applications, there is an urgent need for the understanding of the nanoparticle toxicity and other risks involved with these nanoparticles to human health. In this study, we use large-scale molecular dynamics simulations to study the interaction between several proteins (WW domains) and carbon nanotubes (one form of hydrophobic nanopartides). We have found that the carbon nanotube can plug into the hydrophobic core of proteins to form stable complexes. This plugging of nanotubes disrupts and blocks the active sites of WW domains from binding to the corresponding ligands, thus leading to the loss of the original function of the proteins. The key to this observation is the hydrophobic Interaction between the nanoparticle and the hydrophobic residues, particularly tryptopha
ns, in the core of the domain. We believe that these findings might provide a novel route to the nanopartide toxicity on the molecular level for the hydrophobic nanopartides.

Reprint Address:
Zhou, RH, IBM Corp, Thomas J Watson Res Ctr, Yorktown Hts, NY 10598 USA.

Research Institution addresses:
[Zhou, Ruhong] IBM Corp, Thomas J Watson Res Ctr, Yorktown Hts, NY 10598 USA; [Zuo, Guanghong; Wei, Guanghong; Fang, Haiping] Fudan Univ, T Life Res Ctr, Dept Phys, Shanghai 200433, Peoples R China; [Zuo, Guanghong; Huang, Qing; Fang, Haiping] Chinese Acad Sci, Shanghai Inst Appl Phys, Shanghai 201800, 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:
64

Times Cited:
0

Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA

Subject Category:
Chemistry, Multidisciplinary; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary

ISSN:
1936-0851

DOI:
10.1021/nn101762b

IDS Number:
696NW

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Thursday, January 6, 2011

ISI Web of Knowledge Alert - Hummer, G

ISI Web of Knowledge Citation Alert

Cited Article: Hummer, G. Water conduction through the hydrophobic channel of a carbon nanotube
Alert Expires: 22 AUG 2011
Number of Citing Articles: 1 new records this week (1 in this e-mail)
Organization ID: 3b97d1bbc1878baed0ab183d8b03130b
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Note: Instructions on how to purchase the full text of an article and Help Desk Contact information are at the end of the e-mail.
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Title:
Kinetics of water filling the hydrophobic channels of narrow carbon nanotubes studied by molecular dynamics simulations

Authors:
Wu, KF; Zhou, B; Xiu, P; Qi, WP; Wan, RZ; Fang, HP

Author Full Names:
Wu, Kefei; Zhou, Bo; Xiu, Peng; Qi, Wenpeng; Wan, Rongzheng; Fang, Haiping

Source:
JOURNAL OF CHEMICAL PHYSICS 133 (20): Art. No. 204702 NOV 28 2010

Language:
English

Document Type:
Article

KeyWords Plus:
LIQUID WATER; NANOPORES; MECHANISM; COEXISTENCE; PERMEATION; CONDUCTION; TRANSPORT; MEMBRANES; SYSTEMS; ICE

Abstract:
The kinetics of water filling narrow single-walled carbon nanotubes was studied using molecular dynamics simulations. The time required to fully fill a nanotube was linear with respect to the tube length. We observed that water molecules could enter into nanotubes of different lengths, either from one end or from both ends. The probability of having a nanotube filled completely from both ends increased exponentially with the tube length. For short tubes, filling usually proceeded from only one end. For long tubes, filling generally proceeded from both tube ends over three stages, i.e., filling from one end, filling from both ends, and filling from both ends with the dipole reorientation of water molecules to give a concerted ordering within the fully filled tube. The water molecules in the partially filled nanotube were hydrogen bonded similarly to those in the fully filled nanotube. Simulations for the reference Lennard-Jones fluid without hydrogen bonds were also performed
and showed that the filling behavior of water molecules can be attributed to strong intermolecular hydrogen bonding. (C) 2010 American Institute of Physics. [doi:10.1063/1.3509396]

Reprint Address:
Fang, HP, Chinese Acad Sci, Shanghai Inst Appl Phys, POB 800-204, Shanghai 201800, Peoples R China.

Research Institution addresses:
[Wu, Kefei; Zhou, Bo; Qi, Wenpeng; Wan, Rongzheng; Fang, Haiping] Chinese Acad Sci, Shanghai Inst Appl Phys, Shanghai 201800, Peoples R China; [Wu, Kefei; Zhou, Bo] Chinese Acad Sci, Grad Sch, Beijing 100080, Peoples R China; [Xiu, Peng] Zhejiang Univ, Dept Phys, Bio X Lab, Hangzhou 310027, Peoples R China; [Qi, Wenpeng] Shandong Univ, Sch Phys, Jinan 250100, Peoples R China; [Fang, Haiping] CAS, TPCSF, Beijing 100049, Peoples R China

E-mail Address:
fanghaiping@sinap.ac.cn

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Cited Reference Count:
48

Times Cited:
0

Publisher:
AMER INST PHYSICS; CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA

Subject Category:
Physics, Atomic, Molecular & Chemical

ISSN:
0021-9606

DOI:
10.1063/1.3509396

IDS Number:
690LB

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Friday, December 17, 2010

ISI Web of Knowledge Alert - Hummer, G

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Cited Article: Hummer, G. Water conduction through the hydrophobic channel of a carbon nanotube
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Title:
The structural basis of function in Cys-loop receptors

Authors:
Thompson, AJ; Lester, HA; Lummis, SCR

Author Full Names:
Thompson, Andrew J.; Lester, Henry A.; Lummis, Sarah C. R.

Source:
QUARTERLY REVIEWS OF BIOPHYSICS 43 (4): 449-499 NOV 2010

Language:
English

Document Type:
Review

KeyWords Plus:
NICOTINIC ACETYLCHOLINE-RECEPTOR; GATED ION CHANNELS; PROTEIN-KINASE-C; BENZODIAZEPINE BINDING-SITE; AMINOBUTYRIC ACID(A) RECEPTORS; RECOMBINANT 5-HT3 RECEPTOR; CATION-PI INTERACTIONS; POSITIVE ALLOSTERIC MODULATION; MAJOR INTRACELLULAR DOMAINS; MEMBRANE-SPANNING SEGMENT

Abstract:
Cys-loop receptors are membrane-spanning neurotransmitter-gated ion channels that are responsible for fast excitatory and inhibitory transmission in the peripheral and central nervous systems. The best studied members of the Cys-loop family are nACh, 5-HT3, GABA(A) and glycine receptors. All these receptors share a common structure of five subunits, pseudo-symmetrically arranged to form a rosette with a central ion-conducting pore. Some are cation selective (e.g. nACh and 5-HT3) and some are anion selective (e.g. GABA(A) and glycine). Each receptor has an extracellular domain (ECD) that contains the ligand-binding sites, a transmembrane domain (TMD) that allows ions to pass across the membrane, and an intracellular domain (ICD) that plays a role in channel conductance and receptor modulation. Cys-loop receptors are the targets for many currently used clinically relevant drugs (e.g. benzodiazepines and anaesthetics). Understanding the molecular mechanisms of these receptors co
uld therefore provide the catalyst for further development in this field, as well as promoting the development of experimental techniques for other areas of neuroscience. In this review, we present our current understanding of Cys-loop receptor structure and function. The ECD has been extensively studied. Research in this area has been stimulated in recent years by the publication of high-resolution structures of nACh receptors and related proteins, which have permitted the creation of many Cys loop receptor homology models of this region. Here, using the 5-HT3 receptor as a typical member of the family, we describe how homology modelling and ligand docking can provide useful but not definitive information about ligand interactions. We briefly consider some of the many Cys-loop receptors modulators. We discuss the current understanding of the structure of the TMD, and how this links to the ECD to allow channel gating, and consider the roles of the ICD, whose structure is poo
rly understood. We also describe some of the current methods!
that ar
e beginning to reveal the differences between different receptor states, and may ultimately show structural details of transitions between them.

Reprint Address:
Lummis, SCR, Univ Cambridge, Dept Biochem, Bldg O,Downing Site, Cambridge CB2 1QW, England.

Research Institution addresses:
[Thompson, Andrew J.; Lummis, Sarah C. R.] Univ Cambridge, Dept Biochem, Cambridge CB2 1QW, England; [Lester, Henry A.] CALTECH, Pasadena, CA 91125 USA

E-mail Address:
sl120@cam.ac.uk

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Cited Reference Count:
398

Times Cited:
0

Publisher:
CAMBRIDGE UNIV PRESS; 32 AVENUE OF THE AMERICAS, NEW YORK, NY 10013-2473 USA

Subject Category:
Biophysics

ISSN:
0033-5835

DOI:
10.1017/S0033583510000168

IDS Number:
686PA

========================================================================

*Record 2 of 5.
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*Order Full Text [ ]

Title:
Single-file water as a one-dimensional Ising model

Authors:
Kofinger, J; Dellago, C

Author Full Names:
Koefinger, Juergen; Dellago, Christoph

Source:
NEW JOURNAL OF PHYSICS 12: Art. No. 093044 SEP 27 2010

Language:
English

Document Type:
Article

KeyWords Plus:
CARBON NANOTUBE MEMBRANES; ICE-NANOTUBES; ORDERED WATER; CONDUCTION; PERMEATION; TRANSPORT; CHANNEL; PORES

Abstract:
We show that single-file water in nanopores can be viewed as a one-dimensional (1D) Ising model, and we investigate, on the basis of this, the static dielectric response of a chain of hydrogen-bonded water molecules to an external field. To achieve this, we use a recently developed dipole lattice model that accurately captures the free energetics of nanopore water. In this model, the total energy of the system can be expressed as the sum of the effective interactions of chain ends and orientational defects. Neglecting these interactions, we essentially obtain the 1D Ising model, which allows us to derive analytical expressions for the free energy as a function of the total dipole moment and for the dielectric susceptibility. Our expressions, which agree very well with simulation results, provide the basis for the interpretation of future dielectric spectroscopy experiments on water-filled nanopore membranes.

Reprint Address:
Kofinger, J, NIDDKD, Chem Phys Lab, NIH, Bldg 5, Bethesda, MD 20892 USA.

Research Institution addresses:
[Koefinger, Juergen] NIDDKD, Chem Phys Lab, NIH, Bethesda, MD 20892 USA; [Dellago, Christoph] Univ Vienna, Fac Phys, A-1090 Vienna, Austria

E-mail Address:
koefingerj@mail.nih.gov

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Cited Reference Count:
35

Times Cited:
1

Publisher:
IOP PUBLISHING LTD; DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND

Subject Category:
Physics, Multidisciplinary

ISSN:
1367-2630

DOI:
10.1088/1367-2630/12/9/093044

IDS Number:
687FV

========================================================================

*Record 3 of 5.
*View Full Record: http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000284688700008
*Order Full Text [ ]

Title:
Solvation dynamics of Coumarin 153 in SDS dispersed single walled carbon nanotubes (SWNTs)

Authors:
Sengupta, A; Hazra, P

Author Full Names:
Sengupta, Abhigyan; Hazra, Partha

Source:
CHEMICAL PHYSICS LETTERS 501 (1-3): 33-38 DEC 6 2010

Language:
English

Document Type:
Article

KeyWords Plus:
ANGLE NEUTRON-SCATTERING; ICE-NANOTUBES; LIQUID WATER; MICELLES; SURFACTANTS; SHELL

Abstract:
We have studied the solvation dynamics and rotational relaxation of Coumarin 153 (C-153) in SDS dispersed two different types of single walled carbon nanotubes (SWNTs), namely metallic and semiconducting, using picosecond fluorescence spectroscopy. It has been observed that solvation dynamics of C-153 in SWNTs is severely retarded compared to pure water and SDS micelle. Time resolved fluorescence anisotropy study suggests that C-153 molecules are located on the surface of SWNT, where the rotational motion of the probe is severely hindered compared to SDS micelle due to the restriction imposed by SWNT surface as well as surrounding SDS monomers or SDS half-cylindrical micelles adsorbed on SWNT surface. (C) 2010 Elsevier B. V. All rights reserved.

Reprint Address:
Hazra, P, Indian Inst Sci Educ & Res, Dept Chem, Pune 411021, Maharashtra, India.

Research Institution addresses:
[Sengupta, Abhigyan; Hazra, Partha] Indian Inst Sci Educ & Res, Dept Chem, Pune 411021, Maharashtra, India

E-mail Address:
p.hazra@iiserpune.ac.in

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Cited Reference Count:
31

Times Cited:
0

Publisher:
ELSEVIER SCIENCE BV; PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS

Subject Category:
Chemistry, Physical; Physics, Atomic, Molecular & Chemical

ISSN:
0009-2614

DOI:
10.1016/j.cplett.2010.10.049

IDS Number:
686HZ

========================================================================

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Title:
Self-Assembly and Its Impact on Interfacial Charge Transfer in Carbon Nanotube/P3HT Solar Cells

Authors:
Bernardi, M; Giulianini, M; Grossman, JC

Author Full Names:
Bernardi, Marco; Giulianini, Michele; Grossman, Jeffrey C.

Source:
ACS NANO 4 (11): 6599-6606 NOV 2010

Language:
English

Document Type:
Article

Author Keywords:
self assembly; organic photovoltaics; excitonic solar cells; bulk heterojunction; P3HT; conjugation length; carbon nanotube; molecular dynamics; charge transfer

KeyWords Plus:
MOLECULAR-DYNAMICS; FORCE-FIELD; COMPOSITES; MORPHOLOGY; PROGRESS; SYSTEMS

Abstract:
Charge transfer at the interface of conjugated polymer and nanoscale inorganic acceptors is pivotal in determining the efficiency of exatonic solar cells. Despite intense efforts carbon nanotube/polymer solar cells have resulted in disappointing efficiencies (<2%) due in large part to poor charge transfer at the interface. While the interfacial energy level alignment is clearly important, the self assembly and the interface structure also play a major role in facilitating this charge transfer To understand and control this effect to our advantage, we Study the interface of commonly used conductive polymer poly 3 hexylthiophene (P3HT) and single-walled carbon nanotubes (SWNTs) with a combination of Molecular dynamics simulations, absorption spectra experiments, and an analysis of charge transfer effects classical molecular dynamics simulations show that the P3HT wraps around the SWNTs In a number different conformations, including helices, bundles, and more elongated conformat
ions that maximize planar pi-pi stacking, in agreement with recent experimental observations. Snapshots from the MD simulations reveal that the carbo nanotubes play an important templating role of increasing the pi conjugation in the system, an effect deriving from the pi-pi stacking interaction at the interface and the 1 dimensional (1D) nature of the SWNTs, and independent of the SWNT chirality. We show how this increase in the system for improved preparation of polymeric solar cells based on carbon nanotubes and on 1D system conjugation could largely improve the charge transfer in P3HT-SWNT type II heterojunctions support our our results with absorption spectra measurements of mixtures of carbon nanotubes and P3HT. These findings nanomaterials in general

Reprint Address:
Grossman, JC, MIT, Dept Mat Sci & Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA.

Research Institution addresses:
[Bernardi, Marco; Grossman, Jeffrey C.] MIT, Dept Mat Sci & Engn, Cambridge, MA 02139 USA; [Giulianini, Michele] Queensland Univ Technol, Sch Engn Syst, Brisbane, Qld 4001, Australia

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Times Cited:
0

Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA

Subject Category:
Chemistry, Multidisciplinary; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary

ISSN:
1936-0851

DOI:
10.1021/nn1018297

IDS Number:
682YD

========================================================================

*Record 5 of 5.
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Title:
High-Performance Separation of Nanoparticles with Ultrathin Porous Nanocrystalline Silicon Membranes

Authors:
Gaborski, TR; Snyder, JL; Striemer, CC; Fang, DZ; Hoffman, M; Fauchet, PM; McGrath, JL

Author Full Names:
Gaborski, Thomas R.; Snyder, Jessica L.; Striemer, Christopher C.; Fang, David Z.; Hoffman, Michael; Fauchet, Philippe M.; McGrath, James L.

Source:
ACS NANO 4 (11): 6973-6981 NOV 2010

Language:
English

Document Type:
Article

Author Keywords:
purification; thin film; semiconductor; microfluidics; nanofluidics

KeyWords Plus:
CARBON NANOTUBE MEMBRANES; ANION-EXCHANGE MEMBRANES; ULTRAFILTRATION MEMBRANES; ANGSTROM RESOLUTION; CRYSTAL-STRUCTURE; PLASMID DNA; FILTRATION; TRANSPORT; WATER; FLOW

Abstract:
Porous nanocystalline silicon (pnc Si) is a 15 nm thin free standing membrane material with Applications in small scale separations, biosensors, cell culture, and lab-on a-chip devices Pnc Si has already been shown to exhibit high permeability to diffusing species and selectivity based on molecular size or charge. In this report, we characterize properties of pc Si In pressurized flows We compare results to long standing theories for through short pores using actual pore distributions kilned directly from electron micrographs The measured water permeability is in agreement with theory over a wide range of pore sizes and porosities and orders of magnitude higher than those exhibited by commercial ultrafiltration and experimental carbon nanotube membranes We also show that pnc Si membranes can be used in dead end filtration to,fractionate gold nanoparticles and protein size ladders with better than 5 nm resolution, insignificant sample loss, and little dilution of the filtrate
These performance characteristics, combined with scalable manufacturing, make pnc Si filtration a straightforward solution to many nanoparticle and biological separation problems

Reprint Address:
McGrath, JL, Univ Rochester, Dept Biomed Engn, 601 Elmwood Ave, Rochester, NY 14627 USA.

Research Institution addresses:
[Gaborski, Thomas R.; Hoffman, Michael; McGrath, James L.] Univ Rochester, Dept Biomed Engn, Rochester, NY 14627 USA; [Snyder, Jessica L.] Univ Rochester, Dept Biochem & Biophys, Rochester, NY 14627 USA; [Gaborski, Thomas R.; Striemer, Christopher C.] SiMPore Inc, W Henrietta, NY 14586 USA; [Striemer, Christopher C.; Fang, David Z.; Fauchet, Philippe M.] Univ Rochester, Dept Elect & Comp Engn, Rochester, NY 14627 USA

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Cited Reference Count:
43

Times Cited:
0

Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA

Subject Category:
Chemistry, Multidisciplinary; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary

ISSN:
1936-0851

DOI:
10.1021/nn102064c

IDS Number:
682YD

Please enter your account number here:

Friday, December 10, 2010

ISI Web of Knowledge Alert - Hummer, G

ISI Web of Knowledge Citation Alert

Title:
Pore opening and closing of a pentameric ligand-gated ion channel

Authors:
Zhu, FQ; Hummer, G

Author Full Names:
Zhu, Fangqiang; Hummer, Gerhard

Source:
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 107 (46): 19814-19819 NOV 16 2010

Language:
English

Document Type:
Article

Author Keywords:
ELIC; nicotinic acetylcholine receptor; hydrophobic gate; conformational change; string method

KeyWords Plus:
NICOTINIC ACETYLCHOLINE-RECEPTOR; MOLECULAR-DYNAMICS SIMULATIONS; X-RAY-STRUCTURE; STRING METHOD; CONDUCTION; STATE; PERMEATION; TRANSITION; GRAMICIDIN; HOMOLOG

Abstract:
Nerve signaling in humans and chemical sensing in bacteria both rely on the controlled opening and closing of the ion-conducting pore in pentameric ligand-gated ion channels. With the help of a multiscale simulation approach that combines mixed elastic network model calculations with molecular dynamics simulations, we study the opening and closing of the pore in Gloeobacter violaceus channel GLIC at atomic resolution. In our simulations of the GLIC transmembrane domain, we first verify that the two endpoints of the transition are open and closed to sodium ion conduction, respectively. We then show that a two-stage tilting of the pore-lining helices induces cooperative drying and iris-like closing of the channel pore. From the free energy profile of the gating transition and from unrestrained simulations, we conclude that the pore of the isolated GLIC transmembrane domain closes spontaneously. The mechanical work of opening the pore is performed primarily on the M2-M3 loop. St
rong interactions of this short and conserved loop with the extracellular domain are therefore crucial to couple ligand binding to channel opening.

Reprint Address:
Hummer, G, NIDDKD, Chem Phys Lab, NIH, Bldg 2, Bethesda, MD 20892 USA.

Research Institution addresses:
[Zhu, Fangqiang; Hummer, Gerhard] NIDDKD, Chem Phys Lab, NIH, Bethesda, MD 20892 USA

E-mail Address:
hummer@helix.nih.gov

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Cited Reference Count:
33

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.1009313107

IDS Number:
680UT

========================================================================

Title:
Microscopic properties of nanopore water from its time-dependent dielectric response

Authors:
Kofinger, J; Dellago, C

Author Full Names:
Koefinger, Juergen; Dellago, Christoph

Source:
PHYSICAL REVIEW B 82 (20): Art. No. 205416 NOV 10 2010

Language:
English

Document Type:
Article

KeyWords Plus:
CARBON NANOTUBE MEMBRANES; BORON-NITRIDE NANOTUBE; PROTON CONDUCTION; MASS-TRANSPORT; ISING-MODEL; DYNAMICS; CHANNEL; PERMEATION; SIMULATION; AQUAPORIN-1

Abstract:
We present a simple kinetic model for the orientational dynamics of a chain of hydrogen-bonded molecules due to the diffusion of orientational defects. We derive an event-driven algorithm which allows us to do kinetic simulations for chains from nanoscopic to macroscopic lengths, spanning huge orders of magnitude in time. Our simulations and analytical calculations show that nanopore water exhibits Debye behavior arising from the diffusive dynamics of orientational defects. For the limits of short and long chains we derive analytical expressions for the relaxation times which allow to extract the diffusion constant, the effective interaction, and the excitation energy of these defects from dielectric spectroscopy experiments. We also discuss the possibility to use such experiments to detect if the two possible kinds of orientational defects differ in excitation energy and diffusion constant.

Reprint Address:
Kofinger, J, NIDDK, Chem Phys Lab, NIH, Bldg 5, Bethesda, MD 20892 USA.

Research Institution addresses:
[Koefinger, Juergen] NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USA; [Dellago, Christoph] Univ Vienna, Fac Phys, A-1090 Vienna, Austria

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Cited Reference Count:
53

Times Cited:
0

Publisher:
AMER PHYSICAL SOC; ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA

Subject Category:
Physics, Condensed Matter

ISSN:
1098-0121

DOI:
10.1103/PhysRevB.82.205416

IDS Number:
678CS

========================================================================

Title:
Molecular dynamics simulation of nanoscale liquid flows

Authors:
Li, YX; Xu, JL; Li, DQ

Author Full Names:
Li, Yuxiu; Xu, Jinliang; Li, Dongqing

Source:
MICROFLUIDICS AND NANOFLUIDICS 9 (6): 1011-1031 DEC 2010

Language:
English

Document Type:
Review

Author Keywords:
Molecular dynamics simulation; Liquid flow; Nanochannels; Nanofluidics

KeyWords Plus:
FLUID-SOLID INTERFACE; CARBON NANOTUBES; BOUNDARY-CONDITIONS; ELECTROKINETIC TRANSPORT; ATOMISTIC SIMULATION; NANOFLUIDIC CHANNELS; SURFACE-ROUGHNESS; SHEAR-FLOW; WATER; SLIP

Abstract:
Molecular dynamics (MD) simulation is a powerful tool to investigate the nanoscale fluid flow. In this article, we review the methods and the applications of MD simulation in liquid flows in nanochannels. For pressure-driven flows, we focus on the fundamental research and the rationality of the model hypotheses. For electrokinetic-driven flows and the thermal-driven flows, we concentrate on the principle of generating liquid motion. The slip boundary condition is one of the marked differences between the macro- and micro-scale flows and the nanoscale flows. In this article, we review the parameters controlling the degree of boundary slip and the new findings. MD simulation is based on the Newton's second law to simulate the particles' interactions and consists of several important processing methods, such as the thermal wall model, the cut-off radius, and the initial condition. Therefore, we also reviewed the recent improvement in these key methods to make the MD simulation m
ore rational and efficient. Finally, we summarized the important discoveries in this research field and proposed some worthwhile future research directions.

Reprint Address:
Li, DQ, Univ Waterloo, Dept Mech & Mech Engn, Waterloo, ON N2L 3G1, Canada.

Research Institution addresses:
[Li, Dongqing] Univ Waterloo, Dept Mech & Mech Engn, Waterloo, ON N2L 3G1, Canada; [Li, Yuxiu] Chinese Acad Sci, Guangzhou Inst Energy Convers, Guangzhou 510640, Peoples R China; [Xu, Jinliang] N China Elect Power Univ, Beijing Key Lab New & Renewable Energy, Beijing 102206, Peoples R China

E-mail Address:
dongqing@mme.uwaterloo.ca

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Times Cited:
0

Publisher:
SPRINGER HEIDELBERG; TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY

Subject Category:
Nanoscience & Nanotechnology; Instruments & Instrumentation; Physics, Fluids & Plasmas

ISSN:
1613-4982

DOI:
10.1007/s10404-010-0612-5

IDS Number:
681RZ

========================================================================

Title:
Lubrication by molecularly thin water films confined between nanostructured membranes

Authors:
Kalra, A; Garde, S; Hummer, G

Author Full Names:
Kalra, A.; Garde, S.; Hummer, G.

Source:
EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS 189 (1): 147-154 OCT 2010

Language:
English

Document Type:
Article

KeyWords Plus:
BOUNDARY LUBRICATION; LAYERING TRANSITIONS; SUBNANOMETER FILMS; CARBON NANOTUBE; LIQUID-FILMS; DYNAMICS; FLUIDITY; SURFACES; DEPENDENCE; SIMULATION

Abstract:
We use molecular dynamics simulations to study thermal sliding of two nanostructured surfaces separated by nanoscale water films. We find that friction at molecular separations is determined primarily by the effective free energy landscape for motion in the plane of sliding, which depends sensitively on the surface character and the molecular structure of the confined water. Small changes in the surface nanostructure can have dramatic effects on the apparent rheology. Whereas porous and molecularly rough interfaces of open carbon nanotube membranes are found to glide with little friction, a comparably smooth interface of end-capped nanotubes is effectively stuck. The addition of salt to the water layer is found to reduce the sliding friction. Surprisingly, the intervening layers of water remain fluid in all cases, even in the case of high apparent friction between the two membranes.

Reprint Address:
Kalra, A, Shell Oil Co, Houston, TX 77252 USA.

Research Institution addresses:
[Kalra, A.; Garde, S.] Rensselaer Polytech Inst, Howard P Isermann Dept Chem & Biol Engn, Troy, NY 12180 USA; [Kalra, A.; Hummer, G.] NIDDKD, Chem Phys Lab, NIH, Bethesda, MD 20892 USA

E-mail Address:
gardes@rpi.edu; gerhard.hummer@nih.gov

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Cited Reference Count:
34

Times Cited:
0

Publisher:
SPRINGER HEIDELBERG; TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY

Subject Category:
Physics, Multidisciplinary

ISSN:
1951-6355

DOI:
10.1140/epjst/e2010-01317-9

IDS Number:
678SQ

========================================================================

Title:
Control Performance and Biomembrane Disturbance of Carbon Nanotube Artificial Water Channels by Nitrogen-Doping

Authors:
Yang, YL; Li, XY; Jiang, JL; Du, HL; Zhao, LN; Zhao, YL

Author Full Names:
Yang, Yuling; Li, Xiaoyi; Jiang, Jinliang; Du, Huailiang; Zhao, Lina; Zhao, Yuliang

Source:
ACS NANO 4 (10): 5755-5762 OCT 2010

Language:
English

Document Type:
Article

Author Keywords:
N-SWCNT; N-DWCNT; artificial water channel; water flow control; molecular dynamics simulation

KeyWords Plus:
MOLECULAR-DYNAMICS; PERMEATION; TRANSPORT; NANOMATERIALS; SIMULATIONS; AQUAPORIN-1; CONDUCTION; MECHANISM; DIFFUSION; MEMBRANES

Abstract:
To establish ways to control the performance of artificial water channels is a big challenge. With molecular dynamics studies, we found that water flow inside the water channels of carbon nanotubes (CNTs) can be controlled by reducing or intensifying interaction energy between water molecules and the wall of the CNTs channel. A way of example toward this significant goal was demonstrated by the doping of nitrogen into the wall of CNTs. Different ratios of nitrogen doping result in different controllable water performance which is dominated mainly through a gradient of van der Waals forces created by the heteroatom doping in the wall of CNTs. Further results revealed that the nitrogen-doped CNT channels show less influence on the integrality of biomembrane than the pristine one, while the nitrogen-doped double-walled carbon nanotube exhibits fewer disturbances to the cellular membrane integrality than the nitrogen-doped single-walled carbon nanotube when interacting with biome
mbranes.

Reprint Address:
Li, XY, Chinese Acad Sci, Grad Univ, Coll Mat Sci & Optoelect Technol, Beijing 100049, Peoples R China.

Research Institution addresses:
[Yang, Yuling; Li, Xiaoyi; Du, Huailiang] Chinese Acad Sci, Grad Univ, Coll Mat Sci & Optoelect Technol, Beijing 100049, Peoples R China; [Jiang, Jinliang] Chinese Acad Sci, Grad Univ, Coll Chem & Chem Engn, Beijing 100049, Peoples R China; [Yang, Yuling; Li, Xiaoyi; Zhao, Lina; Zhao, Yuliang] Chinese Acad Sci, Key Lab Biomed Effects Nanomat & Nanosafetey, Inst High Energy Phys, Beijing 100049, Peoples R China; [Yang, Yuling; Li, Xiaoyi; Zhao, Lina; Zhao, Yuliang] Natl Ctr Nanosci & Technol China, Beijing 100049, Peoples R China

E-mail Address:
lixy@gucas.ac.cn; zhaoyuliang@ihep.ac.cn

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Cited Reference Count:
54

Times Cited:
0

Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA

Subject Category:
Chemistry, Multidisciplinary; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary

ISSN:
1936-0851

DOI:
10.1021/nn1014825

IDS Number:
670UV

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