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.

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

Computer-Generated Structural Models for a-Si:H

1988 ◽  
Vol 141 ◽  
Author(s):  
Laurent J. Lewis ◽  
Normand Mousseau ◽  
FranÇois Drolet
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Amorphous Silicon ◽  
Periodic Boundary ◽  
Hydrogenated Amorphous Silicon ◽  
Structural Models ◽  
Periodic Boundary Conditions ◽  
Dynamics Simulations ◽  
Hydrogenated Amorphous ◽  
Good Agreement

AbstractA new algorithm for generating fully-coordinated hydrogenated amorphous silicon models with periodic boundary conditions is presented. The hydrogen is incorporated into an a-Si matrix by a bond-switching process similar to that proposed by Wooten, Winer, and Weaire, making sure that four-fold coordination is preserved and that no rings with less than 5 members are created. After each addition of hydrogen, the structure is fully relaxed. The models so obtained, to be used as input to molecular dynamics simulations, are found to be in good agreement with experiment. A model with 12 at.% H is discussed in detail.

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.

scholarly journals Systematic Finite-Temperature Reduction of Crystal Energy Landscapes.

2020 ◽  
Author(s):  
Nicholas Francia ◽  
Louise S. Price ◽  
Jonas Nyman ◽  
Sarah (Sally) Price ◽  
Matteo Salvalaglio
Keyword(s):  
Molecular Dynamics ◽  
Finite Temperature ◽  
Structure Prediction ◽  
Lattice Energy ◽  
Biased Sampling ◽  
Energy Landscapes ◽  
Polymorphic Transformations ◽  
Temperature And Pressure ◽  
Dynamics Simulations ◽  
The Impact

<p>Crystal structure prediction methods are prone to overestimate the number of potential polymorphs of organic molecules. In this work, we aim to reduce the overprediction by systematically applying molecular dynamics simulations and biased sampling methods to cluster subsets of structures that can easily interconvert at finite temperature and pressure. Following this approach, we rationally reduce the number of predicted putative polymorphs in CSP-generated crystal energy landscapes. This uses an unsupervised clustering approach to analyze independent finite-temperature molecular dynamics trajectories and hence identify a representative structure of each cluster of distinct lattice energy minima that are effectively equivalent at finite temperature and pressure. Biased simulations are used to reduce the impact of limited sampling time and to estimate the work associated with polymorphic transformations. We demonstrate the proposed systematic approach by studying the polymorphs of urea and succinic acid, reducing an initial set of over 100 energetically plausible CSP structures to 12 and 27 respectively, including the experimentally known polymorphs. The simulations also indicate the types of disorder and stacking errors that may occur in real structures.<br></p>

QUASI SYMPLECTIC INTEGRATORS: AN ALTERNATIVE TO NOSÉ HOOVER DYNAMICS?

2005 ◽  
Vol 05 (02) ◽  
pp. L225-L232
Author(s):  
RICCARDO MANNELLA
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Numerical Integration ◽  
Canonical Ensemble ◽  
Symplectic Integrators ◽  
Langevin Equations ◽  
Dynamics Simulations

Quasi symplectic algorithms for the numerical integration of Langevin equations describing systems in a canonical ensemble are discussed. It is shown that they could be an alternative to molecular dynamics simulations done with a Nosé Hoover booster.

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.

Heat Transfer Predictions for Micro/Nano-Channels at Atomistic Level Using Combined Molecular Dynamics and Monte Carlo Techniques

2007 ◽  
Author(s):  
S. V. Nedea ◽  
A. J. Markvoort ◽  
A. A. van Steenhoven ◽  
P. A. J. Hilbers
Keyword(s):  
Molecular Dynamics ◽  
Heat Flux ◽  
Boundary Conditions ◽  
Wall Effects ◽  
Characteristic Parameters ◽  
Monte Carlo Techniques ◽  
Dilute Gas ◽  
Effective Coefficients ◽  
Dynamics Simulations ◽  
Wall Interactions

The thermal behavior of a gas confined between two parallel walls is investigated. Wall effects like hydrophobic or hydrophilic wall interactions are studied, and the effect on the heat flux and other characteristic parameters like density and temperature is shown. For a dilute gas, the dependence on gas-wall interactions of the temperature profile between the walls for the incident and reflected molecules is obtained using Molecular Dynamics. From these profiles, the effective accomodation coefficients for different interactions and different mass fluid/wall ratio are derived. We show that MC with Maxwell boundary conditions based on the accomodation coefficient gives good results for heat flux predictions when compared to pure Molecular Dynamics simulations. We use these effective coefficients to compute the heat flux predictions for a dense gas using MD and MC with Maxwell-like boundary conditions.

Heat Transfer Predictions for Micro-/Nanochannels at the Atomistic Level Using Combined Molecular Dynamics and Monte Carlo Techniques

2009 ◽  
Vol 131 (3) ◽  
Author(s):  
S. V. Nedea ◽  
A. J. Markvoort ◽  
A. A. van Steenhoven ◽  
P. A. J. Hilbers
Keyword(s):  
Molecular Dynamics ◽  
Heat Flux ◽  
Monte Carlo ◽  
Boundary Conditions ◽  
Accommodation Coefficient ◽  
Monte Carlo Techniques ◽  
Effective Coefficients ◽  
Accommodation Coefficients ◽  
Dynamics Simulations ◽  
Wall Interactions

The thermal behavior of a gas confined between two parallel walls is investigated. Wall effects such as hydrophobic or hydrophilic wall interactions are studied, and the effect on the heat flux and other characteristic parameters such as density and temperature is shown. For a dilute gas, the dependence on gas-wall interactions of the temperature profile between the walls for the incident and reflected molecules is obtained using molecular dynamics (MD). From these profiles, the effective accommodation coefficients for different interactions and different mass fluid/wall ratio are derived. We show that Monte Carlo (MC) with Maxwell boundary conditions based on the accommodation coefficient gives good results for heat flux predictions when compared with pure molecular dynamics simulations. We use these effective coefficients to compute the heat flux predictions for a dense gas using MD and MC with Maxwell-like boundary conditions.

Sign in / Sign up

Export Citation Format

Share Document