Cited Article: Majumder M. Nanoscale hydrodynamics - Enhanced flow in carbon nanotubes
Alert Expires: 18 OCT 2009
Number of Citing Articles: 2 new records this week (2 in this e-mail)
Organization ID: 3b97d1bbc1878baed0ab183d8b03130b
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Title:
Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information
Authors:
Calderon, CP; Janosi, L; Kosztin, I
Author Full Names:
Calderon, Christopher P.; Janosi, Lorant; Kosztin, Ioan
Source:
JOURNAL OF CHEMICAL PHYSICS 130 (14): Art. No. 144908 APR 14 2009
Language:
English
Document Type:
Article
Author Keywords:
cellular transport; differential equations; maximum likelihood estimation; molecular biophysics; molecular dynamics method; nonlinear dynamical systems; positive ions; potassium; reaction kinetics theory; reaction-diffusion systems; stochastic processes; time series
KeyWords Plus:
MOLECULAR-DYNAMICS SIMULATIONS; FREE-ENERGY DIFFERENCES; GRAMICIDIN-A; LIKELIHOOD-ESTIMATION; DIFFUSION-MODELS; ION CHANNELS; TIME-SERIES; MEAN FORCE; SYSTEMS; EQUILIBRIUM
Abstract:
We demonstrate how the surrogate process approximation (SPA) method can be used to compute both the potential of mean force along a reaction coordinate and the associated diffusion coefficient using a relatively small number (10-20) of bidirectional nonequilibrium trajectories coming from a complex system. Our method provides confidence bands which take the variability of the initial configuration of the high-dimensional system, continuous nature of the work paths, and thermal fluctuations into account. Maximum-likelihood-type methods are used to estimate a stochastic differential equation (SDE) approximating the dynamics. For each observed time series, we estimate a new SDE resulting in a collection of SPA models. The physical significance of the collection of SPA models is discussed and methods for exploiting information in the population of estimated SPA models are demonstrated and suggested. Molecular dynamics simulations of potassium ion dynamics inside a gramicidin A c!
hannel are used to demonstrate the methodology, although SPA-type modeling has also proven useful in analyzing single-molecule experimental time series [J. Phys. Chem. B 113, 118 (2009)].
Reprint Address:
Calderon, CP, Rice Univ, Dept Computat & Appl Math, Houston, TX 77005 USA.
Research Institution addresses:
[Calderon, Christopher P.] Rice Univ, Dept Computat & Appl Math, Houston, TX 77005 USA; [Janosi, Lorant; Kosztin, Ioan] Univ Missouri, Dept Phys & Astron, Columbia, MO 65211 USA
E-mail Address:
calderon@rice.edu
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Cited Reference Count:
81
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:
10.1063/1.3106225
IDS Number:
439HC
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Title:
Recycling Ultrathin Catalyst Layers for Multiple Single-Walled Carbon Nanotube Array Regrowth Cycles and Selectivity in Catalyst Activation
Authors:
Pint, CL; Nicholas, N; Duque, JG; Parra-Vasquez, ANG; Pasquali, M; Hauge, R
Author Full Names:
Pint, Cary L.; Nicholas, Nolan; Duque, Juan G.; Parra-Vasquez, A. Nicholas G.; Pasquali, Matteo; Hauge, Robert
Source:
CHEMISTRY OF MATERIALS 21 (8): 1550-1556 APR 28 2009
Language:
English
Document Type:
Article
KeyWords Plus:
GROWTH; WATER; CARPETS; FILMS; ADHESIVES
Abstract:
We utilize chemical vapor deposition to demonstrate the reactivation of catalyst for multiple regrowths of vertically aligned carbon nanotube arrays (carpets) in the context of water-assisted supergrowth. The carpets are transferred from the growth substrate, and the catalyst and substrate are reactivated by annealing in air. Annealing parameters control the length and diameter distribution of nanotubes in the regrown carpets due to active catalyst termination followed by a size-dependent process of iron carbide particle reoxidation. The lack of achieving indefinite regrowth from a 0.5 nm thick Fe layer can be attributed to factors such as catalyst dynamics taking place during the growth and regrowth processes.
Reprint Address:
Hauge, R, Rice Univ, Dept Chem, Houston, TX 77005 USA.
Research Institution addresses:
[Pint, Cary L.; Pasquali, Matteo; Hauge, Robert] Rice Univ, Dept Chem, Houston, TX 77005 USA; [Pint, Cary L.; Nicholas, Nolan] Rice Univ, Dept Phys, Houston, TX 77005 USA; [Duque, Juan G.; Parra-Vasquez, A. Nicholas G.; Pasquali, Matteo] Rice Univ, Dept Chem & Biomol Engn, Houston, TX 77005 USA; [Pint, Cary L.; Nicholas, Nolan; Duque, Juan G.; Parra-Vasquez, A. Nicholas G.; Pasquali, Matteo; Hauge, Robert] Rice Univ, Richard E Smalley Inst Nanoscale Sci & Technol, Houston, TX 77005 USA
E-mail Address:
Hauge@rice.edu
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Cited Reference Count:
33
Times Cited:
0
Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Subject Category:
Chemistry, Physical; Materials Science, Multidisciplinary
ISSN:
0897-4756
DOI:
10.1021/cm8031626
IDS Number:
436KG
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