Structural Order in Water: Comparison between the Spectral Analysis of Raman Data and Molecular Dynamics Results

2007 ◽  
Author(s):  
N. Faginas Lago ◽  
M. Paolantoni ◽  
A. Laganá ◽  
M. Alberti ◽  
Theodore E. Simos ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Spectral Analysis ◽  
Structural Order ◽  
Molecular Dynamics Results

Determination of the Stress Distribution at the Interface Metal-Oxide: Numerical and Theoretical Considerations

2005 ◽  
Vol 237-240 ◽  
pp. 145-150 ◽  
Author(s):  
Sébastien Garruchet ◽  
A. Hasnaoui ◽  
Olivier Politano ◽  
Tony Montesin ◽  
J. Marcos Salazar ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Stress Distribution ◽  
Oxide Film ◽  
Metal Oxide ◽  
Reaction Kinetics ◽  
Analytical Model ◽  
Equilibrium Thermodynamics ◽  
Theoretical Considerations ◽  
Molecular Dynamics Results

In this paper we give a brief presentation of the approaches we have recently developed on the oxidation of metals. Firstly, we present an analytical model based on non-equilibrium thermodynamics to describe the reaction kinetics present during the oxidation of a metal. Secondly, we present the molecular dynamics results obtained with a code specially tailored to study the oxidation and growth of an oxide film of aluminium. Our simulations present an excellent agreement with experimental results.

scholarly journals Spectral analysis of molecular dynamics simulations on PDZ: MD sectors

2019 ◽  
Vol 38 (3) ◽  
pp. 781-790
Author(s):  
Bharat Lakhani ◽  
Kelly M. Thayer ◽  
Emily Black ◽  
David L. Beveridge
Keyword(s):  
Molecular Dynamics ◽  
Spectral Analysis ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

Time-dependent vibrational spectral analysis of first principles trajectory of methylamine with wavelet transform

2017 ◽  
Vol 19 (15) ◽  
pp. 9912-9922 ◽  
Author(s):  
Sohag Biswas ◽  
Bhabani S. Mallik
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Spectral Analysis ◽  
First Principles ◽  
Density Functional ◽  
Time Dependent ◽  
Amine Group ◽  
Ambient Conditions ◽  
Functional Theory ◽  
Fluctuation Dynamics

The fluctuation dynamics of amine stretching frequencies, hydrogen bonds, dangling N–D bonds, and the orientation profile of the amine group of methylamine (MA) were investigated under ambient conditions by means of dispersion-corrected density functional theory-based first principles molecular dynamics (FPMD) simulations.

Design and Modeling of a Peptide Based NanoTweezer

2006 ◽  
Author(s):  
Gaurav Sharma ◽  
Kaushal Rege ◽  
Constantinos Mavroidis ◽  
Martin L. Yarmush
Keyword(s):  
Molecular Dynamics ◽  
Coiled Coil ◽  
Computational Results ◽  
Actuation Mechanism ◽  
Electrostatic Charges ◽  
Environmentally Responsive ◽  
Force Profile ◽  
Potential Applications ◽  
Polypeptide Chains ◽  
Molecular Dynamics Results

The design hypothesis, architectures, and preliminary computational results of a peptide based nanoTweezer are presented in this paper. We engineered the α-helical coiled coil portion of the yeast transcriptional activator peptide called GCN4 to obtain an environmentally-responsive nanoTweezer. The dimeric coiled coil peptide consists of two identical ~4.5 nm long and ~3 nm wide polypeptide chains. The actuation mechanism depends on the modifying electrostatic charges along the peptide by varying the pH of the solution resulting in the reversible movement of helices and therefore, creating the motion of the tweezer. Preliminary molecular dynamics results indicated that pH changes led to a reversible deflection of 1–2 nm with the nanoTweezer. The force profile of the nanoTweezer motion and some potential applications are also discussed.

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