Thermal Denaturation of Polyalanine Peptide in Water by Molecular Dynamics Simulations and Theoretical Prediction of Infrared Spectra:  Helix−Coil Transition Kinetics

2007 ◽  
Vol 111 (3) ◽  
pp. 605-617 ◽  
Author(s):  
Seongeun Yang ◽  
Minhaeng Cho
Keyword(s):  
Molecular Dynamics ◽  
Theoretical Prediction ◽  
Molecular Dynamics Simulations ◽  
Infrared Spectra ◽  
Thermal Denaturation ◽  
Coil Transition ◽  
Dynamics Simulations

Finite Temperature Infrared Spectra from Polarizable Molecular Dynamics Simulations

2014 ◽  
Vol 10 (8) ◽  
pp. 3190-3199 ◽  
Author(s):  
David Semrouni ◽  
Ashwani Sharma ◽  
Jean-Pierre Dognon ◽  
Gilles Ohanessian ◽  
Carine Clavaguéra
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Infrared Spectra ◽  
Finite Temperature ◽  
Dynamics Simulations

Improving anharmonic infrared spectra using semiclassically prepared molecular dynamics simulations

2012 ◽  
Vol 14 (7) ◽  
pp. 2381 ◽  
Author(s):  
Nguyen-Thi Van-Oanh ◽  
Cyril Falvo ◽  
Florent Calvo ◽  
David Lauvergnat ◽  
Marie Basire ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Infrared Spectra ◽  
Dynamics Simulations

scholarly journals Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field

2015 ◽  
Vol 17 (39) ◽  
pp. 25968-25977 ◽  
Author(s):  
Florian Thaunay ◽  
Jean-Pierre Dognon ◽  
Gilles Ohanessian ◽  
Carine Clavaguéra
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Infrared Spectra ◽  
Finite Temperature ◽  
Vibrational Mode ◽  
Vibrational Modes ◽  
Polarizable Force Field ◽  
Dynamics Simulations ◽  
Mode Assignment

The Driven Molecular Dynamics approach has been adapted and associated with the AMOEBA polarizable force field to assign and visualize vibrational modes in infrared spectra obtained by molecular dynamics simulations.

Signatures of protein thermal denaturation and local hydrophobicity in domain specific hydration behavior: a comparative molecular dynamics study

2016 ◽  
Vol 12 (4) ◽  
pp. 1139-1150 ◽  
Author(s):  
Prathit Chatterjee ◽  
Neelanjana Sengupta
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thermal Denaturation ◽  
Thermal Conditions ◽  
Heat Denaturation ◽  
Domain Specific ◽  
Surface Hydration ◽  
Local Unfolding ◽  
Dynamics Simulations

We investigate, using atomistic molecular dynamics simulations, the association of surface hydration accompanying local unfolding in the mesophilic protein Yfh1 under a series of thermal conditions spanning its cold and heat denaturation temperatures.

What Far-Infrared Spectra Can Contribute to the Development of Force Fields for Ionic Liquids Used in Molecular Dynamics Simulations

ChemPhysChem ◽  
2009 ◽  
Vol 10 (8) ◽  
pp. 1181-1186 ◽  
Author(s):  
Thorsten Köddermann ◽  
Koichi Fumino ◽  
Ralf Ludwig ◽  
José N. Canongia Lopes ◽  
Agílio A. H. Pádua
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Infrared Spectra ◽  
Force Fields ◽  
Far Infrared ◽  
Dynamics Simulations ◽  
Far Infrared Spectra
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