Free energy and scalings for polymer translocation through a nanopore: A molecular dynamics simulation study combined with milestoning

Xiang-Gui Xue; Li Zhao; Zhong-Yuan Lu; Ze-Sheng Li

doi:10.1016/j.physleta.2011.12.014

Free energy and scalings for polymer translocation through a nanopore: A molecular dynamics simulation study combined with milestoning

Physics Letters A ◽

10.1016/j.physleta.2011.12.014 ◽

2012 ◽

Vol 376 (4) ◽

pp. 290-292 ◽

Cited By ~ 3

Author(s):

Xiang-Gui Xue ◽

Li Zhao ◽

Zhong-Yuan Lu ◽

Ze-Sheng Li

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamics Simulation ◽

Polymer Translocation

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Solid−Liquid Interfacial Free Energy of Water: A Molecular Dynamics Simulation Study

Journal of Chemical Theory and Computation ◽

10.1021/ct600345s ◽

2007 ◽

Vol 3 (4) ◽

pp. 1494-1498 ◽

Cited By ~ 17

Author(s):

Jun Wang ◽

Yuk Wai Tang ◽

X. C. Zeng

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Interfacial Free Energy ◽

Dynamics Simulation ◽

Solid Liquid

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A molecular dynamics simulation study of the crystal–melt interfacial free energy and its anisotropy in the Cu–Ag–Au ternary system

Journal of Crystal Growth ◽

10.1016/j.jcrysgro.2011.05.015 ◽

2011 ◽

Vol 327 (1) ◽

pp. 227-232 ◽

Cited By ~ 21

Author(s):

A.A. Potter ◽

J.J. Hoyt

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Ternary System ◽

Simulation Study ◽

Interfacial Free Energy ◽

Dynamics Simulation

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The mechanism of the effect of U18666a on blocking the activity of 3β-hydroxysterol Δ-24-reductase (DHCR24): molecular dynamics simulation study and free energy analysis

Journal of Molecular Modeling ◽

10.1007/s00894-016-2907-2 ◽

2016 ◽

Vol 22 (2) ◽

Cited By ~ 4

Author(s):

Xiaoping Quan ◽

Xiuqiang Chen ◽

Deliang Sun ◽

Bo Xu ◽

Linlin Zhao ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Energy Analysis ◽

Dynamics Simulation ◽

Free Energy Analysis

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Freezing point and solid-liquid interfacial free energy of Stockmayer dipolar fluids: A molecular dynamics simulation study

The Journal of Chemical Physics ◽

10.1063/1.4821455 ◽

2013 ◽

Vol 139 (11) ◽

pp. 114705 ◽

Cited By ~ 5

Author(s):

Jun Wang ◽

Pankaj A. Apte ◽

James R. Morris ◽

Xiao Cheng Zeng

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Freezing Point ◽

Interfacial Free Energy ◽

Dynamics Simulation ◽

Dipolar Fluids ◽

Solid Liquid

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Free Energy Profile of RNA Hairpins: A Molecular Dynamics Simulation Study

Biophysical Journal ◽

10.1016/j.bpj.2009.10.040 ◽

2010 ◽

Vol 98 (4) ◽

pp. 627-636 ◽

Cited By ~ 45

Author(s):

Nan-Jie Deng ◽

Piotr Cieplak

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamics Simulation ◽

Energy Profile ◽

Free Energy Profile ◽

Rna Hairpins

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Free energy calculations for Lennard-Jones systems and water using the expanded ensemble method A Monte Carlo and molecular dynamics simulation study

Molecular Physics ◽

10.1080/00268979400100344 ◽

1994 ◽

Vol 82 (3) ◽

pp. 455-471 ◽

Cited By ~ 51

Author(s):

Alexander P. Lyubartsev ◽

Aatto Laaksonen ◽

Pavel N. Vorontsov-Velyaminov

Keyword(s):

Molecular Dynamics ◽

Monte Carlo ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Energy Calculations ◽

Lennard Jones ◽

Expanded Ensemble

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Deciphering the Ion Selectivity of the Phosphate Specific Channel OprP from Pseudomonas Aeruginosa: A Free-Energy Molecular Dynamics Simulation Study

Biophysical Journal ◽

10.1016/j.bpj.2012.11.3456 ◽

2013 ◽

Vol 104 (2) ◽

pp. 624a

Author(s):

Niraj Modi ◽

Roland Benz ◽

Robert E.W. Hancock ◽

Ulrich Kleinekathöfer

Keyword(s):

Molecular Dynamics ◽

Pseudomonas Aeruginosa ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Ion Selectivity ◽

Dynamics Simulation

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Molecular Dynamics Simulation Study on CO2 Physical Absorption Mechanisms for Ethylene-Glycol-Based Solvents Using Free Energy Calculations

Industrial & Engineering Chemistry Research ◽

10.1021/acs.iecr.6b01074 ◽

2016 ◽

Vol 55 (29) ◽

pp. 8200-8206 ◽

Cited By ~ 4

Author(s):

Ryo Nagumo ◽

Yukihiro Muraki ◽

Shuichi Iwata ◽

Hideki Mori ◽

Hiromitsu Takaba ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Ethylene Glycol ◽

Simulation Study ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Energy Calculations ◽

Physical Absorption

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Molecular Dynamics Simulation Study of 18-Crown-6 in Aqueous Solution. 2. Free Energy Profile for the Association 18C6.cntdot. .cntdot. .cntdot.K+ in Water

The Journal of Physical Chemistry ◽

10.1021/j100015a003 ◽

1995 ◽

Vol 99 (15) ◽

pp. 5240-5246 ◽

Cited By ~ 16

Author(s):

Thomas Kowall ◽

Alfons Geiger

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamics Simulation ◽

Energy Profile ◽

Free Energy Profile

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Treatment of rotational isomers in free energy calculations. II. Molecular dynamics simulation study of 18‐crown‐6 in aqueous solution as an example of systems with large numbers of rotational isomeric states

The Journal of Chemical Physics ◽

10.1063/1.456896 ◽

1989 ◽

Vol 91 (6) ◽

pp. 3631-3637 ◽

Cited By ~ 62

Author(s):

T. P. Straatsma ◽

J. A. McCammon

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Energy Calculations ◽

Rotational Isomers ◽

Large Numbers

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