Free Energy Landscape of a DNA−Carbon Nanotube Hybrid Using Replica Exchange Molecular Dynamics

Robert R. Johnson; Axel Kohlmeyer; A. T. Charlie Johnson; Michael L. Klein

doi:10.1021/nl802645d

Free Energy Landscape of a DNA−Carbon Nanotube Hybrid Using Replica Exchange Molecular Dynamics

Nano Letters ◽

10.1021/nl802645d ◽

2009 ◽

Vol 9 (2) ◽

pp. 537-541 ◽

Cited By ~ 135

Author(s):

Robert R. Johnson ◽

Axel Kohlmeyer ◽

A. T. Charlie Johnson ◽

Michael L. Klein

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Carbon Nanotube ◽

Energy Landscape ◽

Replica Exchange ◽

Free Energy Landscape ◽

Replica Exchange Molecular Dynamics

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Folding Free-Energy Landscape of α-Synuclein (35–97) Via Replica Exchange Molecular Dynamics

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.0c01278 ◽

2020 ◽

Author(s):

Karnesh Jain ◽

Othman Ghribi ◽

Jerome Delhommelle

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Landscape ◽

Replica Exchange ◽

Free Energy Landscape ◽

Replica Exchange Molecular Dynamics ◽

Folding Free Energy

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Free energy landscape and folding mechanism of a β-hairpin in explicit water: A replica exchange molecular dynamics study

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20696 ◽

2005 ◽

Vol 61 (4) ◽

pp. 795-808 ◽

Cited By ~ 104

Author(s):

Phuong H. Nguyen ◽

Gerhard Stock ◽

Emil Mittag ◽

Chin-Kun Hu ◽

Mai Suan Li

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Landscape ◽

Replica Exchange ◽

Free Energy Landscape ◽

Replica Exchange Molecular Dynamics ◽

Folding Mechanism ◽

Explicit Water

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Comparative study of 3D-RISM theory and molecular dynamics calculations for the free-energy landscape of a hydrated dipeptide

Molecular Simulation ◽

10.1080/08927022.2017.1342128 ◽

2017 ◽

Vol 43 (13-16) ◽

pp. 1406-1411 ◽

Cited By ~ 1

Author(s):

Hiroshi Iwasaki ◽

Satoshi Yamaguchi ◽

Shinichi Miura

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Comparative Study ◽

Energy Landscape ◽

Free Energy Landscape ◽

Molecular Dynamics Calculations

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Structural, molecular motions, and free-energy landscape of Leishmania sterol-14α-demethylase wild type and drug resistant mutant: a comparative molecular dynamics study

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2018.1461135 ◽

2018 ◽

Vol 37 (6) ◽

pp. 1477-1493 ◽

Cited By ~ 8

Author(s):

Saravanan Vijayakumar ◽

Pradeep Das

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Landscape ◽

Resistant Mutant ◽

Free Energy Landscape ◽

Drug Resistant ◽

Molecular Motions ◽

Wild Type ◽

Drug Resistant Mutant

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Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0608432104 ◽

2007 ◽

Vol 104 (12) ◽

pp. 4925-4930 ◽

Cited By ~ 176

Author(s):

H. Lei ◽

C. Wu ◽

H. Liu ◽

Y. Duan

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Energy Landscape ◽

Free Energy Landscape ◽

Villin Headpiece ◽

Dynamics Simulations ◽

Folding Free Energy

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Free Energy Surface of an Intrinsically Disordered Protein: Comparison between Temperature Replica Exchange Molecular Dynamics and Bias-Exchange Metadynamics

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.5b00047 ◽

2015 ◽

Vol 11 (6) ◽

pp. 2776-2782 ◽

Cited By ~ 50

Author(s):

Gül H. Zerze ◽

Cayla M. Miller ◽

Daniele Granata ◽

Jeetain Mittal

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Surface ◽

Intrinsically Disordered Protein ◽

Replica Exchange ◽

Free Energy Surface ◽

Replica Exchange Molecular Dynamics ◽

Intrinsically Disordered ◽

Disordered Protein

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The investigation of the secondary structure propensities and free-energy landscapes of peptide ligands by replica exchange molecular dynamics simulations

Molecular Simulation ◽

10.1080/08927022.2013.835486 ◽

2013 ◽

Vol 40 (13) ◽

pp. 1015-1025 ◽

Cited By ~ 2

Author(s):

Kadir Demir ◽

Nesrin Kılıç ◽

Fahriye Ceyda Dudak ◽

İsmail Hakkı Boyacı ◽

Fatih Yaşar

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Secondary Structure ◽

Molecular Dynamics Simulations ◽

Peptide Ligands ◽

Replica Exchange ◽

Energy Landscapes ◽

Replica Exchange Molecular Dynamics ◽

Free Energy Landscapes ◽

Dynamics Simulations

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A manifestation of the Ostwald step rule: Molecular-dynamics simulations and free-energy landscape of the primary nucleation and melting of single-molecule polyethylene in dilute solution

The Journal of Chemical Physics ◽

10.1063/1.2102889 ◽

2005 ◽

Vol 123 (14) ◽

pp. 144907 ◽

Cited By ~ 18

Author(s):

L. Larini ◽

D. Leporini

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Single Molecule ◽

Energy Landscape ◽

Free Energy Landscape ◽

Dilute Solution ◽

Primary Nucleation ◽

Ostwald Step Rule ◽

Dynamics Simulations

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Determining the free energy landscape of α-synuclein (35-97) using molecular dynamics

10.1021/scimeetings.0c01904 ◽

2020 ◽

Author(s):

Karnesh Jain ◽

Othman Ghribi ◽

Jerome Delhommelle

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Landscape ◽

Free Energy Landscape

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Energy Landscape Mapping and Replica Exchange Molecular Dynamics of an Adsorbed Peptide

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.9b10568 ◽

2020 ◽

Vol 124 (13) ◽

pp. 2527-2538

Author(s):

James A. Ross-Naylor ◽

Milan Mijajlovic ◽

Mark J. Biggs

Keyword(s):

Molecular Dynamics ◽

Energy Landscape ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Landscape Mapping

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