scholarly journals Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations

2018 ◽  
Vol 122 (25) ◽  
pp. 6559-6569 ◽  
Author(s):  
O. H. Samuli Ollila ◽  
Harri A. Heikkinen ◽  
Hideo Iwaï
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Spin Relaxation ◽  
Relaxation Times ◽  
Rotational Dynamics ◽  
Dynamics Simulations

scholarly journals Molecular Rotational Dynamics in Mixed CH4–CO2 Hydrates: Insights from Molecular Dynamics Simulations

2019 ◽  
Vol 123 (43) ◽  
pp. 26251-26262
Author(s):  
Bernadette R. Cladek ◽  
S. Michelle Everett ◽  
Marshall T. McDonnell ◽  
Matthew G. Tucker ◽  
David J. Keffer ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Rotational Dynamics ◽  
Dynamics Simulations

Molecular Dynamics Simulations of Water Confined in Calcite Slit Pores: An NMR Spin Relaxation and Hydrogen Bond Analysis

2017 ◽  
Vol 121 (12) ◽  
pp. 6674-6684 ◽  
Author(s):  
Sylvia M. Mutisya ◽  
Alexsandro Kirch ◽  
James M. de Almeida ◽  
Verónica M. Sánchez ◽  
Caetano R. Miranda
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulations ◽  
Spin Relaxation ◽  
Nmr Spin Relaxation ◽  
Dynamics Simulations ◽  
Slit Pores ◽  
Hydrogen Bond Analysis

Fullerene rotational dynamics generate disordered configurations that suppress thermal conductivity in superatomic crystals

2020 ◽  
Vol 5 (11) ◽  
pp. 1524-1529
Author(s):  
Qi Liang ◽  
Matthew Bartnof ◽  
Ya-Ling He ◽  
Jonathan A. Malen ◽  
Alan J. H. McGaughey
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Orientational Order ◽  
Rotational Dynamics ◽  
Dynamics Simulations

We perform the first-ever molecular dynamics simulations of superatomic crystals (SACs), from which we precisely link orientational order and thermal conductivity by directly observing the rotational dynamics.

scholarly journals A Comparative Study of Intramolecular Mobility of Single Siloxane and Carbosilane Dendrimers via Molecular Dynamics Simulations

Polymers ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 838 ◽  
Author(s):  
Andrey Kurbatov ◽  
Nikolay Balabaev ◽  
Mikhail Mazo ◽  
Elena Kramarenko
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Relaxation Times ◽  
Carbosilane Dendrimers ◽  
Intramolecular Dynamics ◽  
Rotational Angle ◽  
Spacer Length ◽  
Generation Number ◽  
Dynamics Simulations ◽  
Core Functionality

A comparative analysis of intramolecular dynamics of four types of isolated dendrimers from the fourth to the seventh generations belonging to the siloxane and carbosilane families, differing in spacer length, core functionality, and the type of chemical bonds, has been performed via atomic molecular dynamics simulations. The average radial and angular positions of all Si branching atoms of various topological layers within the dendrimer interior, as well as their variations, have been calculated, and the distributions of the relaxation times of their radial and angular motions have been found. It has been shown that the dendrons of all the dendrimers elongate from the center and decrease in a solid angle with an increasing generation number. The characteristic relaxation times of both angular and radial motions of Si atoms are of the order of a few nanoseconds, and they increase with an increasing generation number and decrease with temperature, with the angular relaxation times being larger than the radial ones. The relaxation times in the carbosilanes are larger than those in the siloxanes. The rotational angle dynamics of the carbosilane dendrimers show that the chain bending is mainly realized via trans-gauche transitions in the Si branching bonds.

Predicting Phonon Properties From Molecular Dynamics Simulations Using the Spectral Energy Density

2011 ◽  
Author(s):  
Joseph E. Turney ◽  
John A. Thomas ◽  
Alan J. H. McGaughey ◽  
Cristina H. Amon
Keyword(s):  
Molecular Dynamics ◽  
Energy Density ◽  
Molecular Dynamics Simulations ◽  
Lattice Dynamics ◽  
Relaxation Times ◽  
Mode Analysis ◽  
Spectral Energy ◽  
Spectral Energy Density ◽  
Dynamics Simulations ◽  
Phonon Properties

Using lattice dynamics theory, we derive the spectral energy density and the relation between the spectral energy density and the phonon frequencies and relaxation times. We then calculate the spectral energy density and phonon frequencies and relaxation times for a test system of Lennard-Jones argon using velocities obtained from molecular dynamics simulations. The phonon properties, which can be used to calculate thermal conductivity, are compared to predictions made using (i) anharmonic lattice dynamics calculations and (ii) a technique that performs normal mode analysis on the positions and velocities obtained from molecular dynamics simulations.

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