Variational boundary conditions for molecular dynamics simulations of crystalline solids at finite temperature: Treatment of the thermal bath

2007 ◽  
Vol 76 (10) ◽  
Author(s):  
Xiantao Li ◽  
Weinan E
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Molecular Dynamics Simulations ◽  
Finite Temperature ◽  
Temperature Treatment ◽  
Thermal Bath ◽  
Crystalline Solids ◽  
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

scholarly journals Zero-Point Energy Leakage in Quantum Thermal Bath Molecular Dynamics Simulations

2016 ◽  
Vol 12 (12) ◽  
pp. 5688-5697 ◽  
Author(s):  
Fabien Brieuc ◽  
Yael Bronstein ◽  
Hichem Dammak ◽  
Philippe Depondt ◽  
Fabio Finocchi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Zero Point ◽  
Thermal Bath ◽  
Zero Point Energy ◽  
Point Energy ◽  
Energy Leakage ◽  
Dynamics Simulations

Vibration of Single- and Double-Layered Graphene Sheets

2011 ◽  
Vol 2 (1) ◽  
Author(s):  
Behrouz Arash ◽  
Quan Wang
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Molecular Dynamics Simulations ◽  
Nonlocal Parameter ◽  
Small Scale ◽  
Graphene Sheets ◽  
Elastic Model ◽  
Resonant Frequencies ◽  
Nonlocal Continuum Theory ◽  
Dynamics Simulations

Free vibration of single- and double-layered graphene sheets is investigated by employing nonlocal continuum theory and molecular dynamics simulations. Results show that the classical elastic model overestimated the resonant frequencies of the sheets by a percentage as high as 62%. The dependence of small-scale effects, sizes of sheets, boundary conditions, and number of layers on vibrational characteristic of single- and double-layered graphene sheets is studied. The resonant frequencies predicted by the nonlocal elastic plate theory are verified by the molecular dynamics simulations, and the nonlocal parameter is calibrated through the verification process. The simulation results reveal that the calibrated nonlocal parameter depends on boundary conditions and vibrational modes. The nonlocal plate model is found to be indispensable in vibration analysis of grapheme sheets with a length less than 8 nm on their sides.

Interface Conditions for Coupled Atomistic and Continuum Models of Solids for Dynamics Problems at Finite Temperature

2006 ◽  
Vol 978 ◽  
Author(s):  
Xiantao Li ◽  
Weinan E
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Finite Temperature ◽  
Langevin Equations ◽  
Continuum Models ◽  
Interface Conditions ◽  
System Temperature ◽  
Dynamics Simulations ◽  
Dynamics Problems ◽  
Generalized Langevin Equations

AbstractWe will present a general formalism for deriving boundary conditions for molecular dynamics simulations of crystalline solids in the context of atomistic/continuum coupling. These boundary conditions are modeled by generalized Langevin equations, derived from Mori-Zwanzig's formalism. Such boundary conditions are useful in suppressing phonon reflections, and maintaining the system temperature.

scholarly journals Assessing the capability ofin silicomutation protocols for predicting the finite temperature conformation of amino acids

2018 ◽  
Vol 20 (40) ◽  
pp. 25901-25909 ◽  
Author(s):  
Rodrigo Ochoa ◽  
Miguel A. Soler ◽  
Alessandro Laio ◽  
Pilar Cossio
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulations ◽  
Point Mutation ◽  
Finite Temperature ◽  
Single Point ◽  
Single Point Mutation ◽  
Equilibrium Configurations ◽  
Dynamics Simulations

Single-point mutation protocols based on backbone-dependent rotamer libraries show the best performance in predicting equilibrium configurations from molecular dynamics simulations.

scholarly journals On the Vibration of Single-Walled Carbon Nanocones: Molecular Mechanics Approach versus Molecular Dynamics Simulations

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
R. Ansari ◽  
A. Momen ◽  
S. Rouhi ◽  
S. Ajori
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Molecular Dynamics Simulations ◽  
Natural Frequency ◽  
Structural Method ◽  
Covalent Bonds ◽  
Carbon Nanocones ◽  
Single Walled Carbon ◽  
Vibrational Behavior ◽  
Dynamics Simulations

The vibrational behavior of single-walled carbon nanocones is studied using molecular structural method and molecular dynamics simulations. In molecular structural approach, point mass and beam elements are employed to model the carbon atoms and the connecting covalent bonds, respectively. Single-walled carbon nanocones with different apex angles are considered. Besides, the vibrational behavior of nanocones under various types of boundary conditions is studied. Predicted natural frequencies are compared with the existing results in the literature and also with the ones obtained by molecular dynamics simulations. It is found that decreasing apex angle and the length of carbon nanocone results in an increase in the natural frequency. Comparing the vibrational behavior of single-walled carbon nanocones under different boundary conditions shows that the effect of end condition on the natural frequency is more prominent for nanocones with smaller apex angles.

scholarly journals Nonperiodic stochastic boundary conditions for molecular dynamics simulations of materials embedded into a continuum mechanics domain

2011 ◽  
Vol 134 (15) ◽  
pp. 154108 ◽  
Author(s):  
Mohammad Rahimi ◽  
Hossein Ali Karimi-Varzaneh ◽  
Michael C. Böhm ◽  
Florian Müller-Plathe ◽  
Sebastian Pfaller ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Molecular Dynamics Simulations ◽  
Continuum Mechanics ◽  
Dynamics Simulations ◽  
Stochastic Boundary
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