Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation

2011 ◽  
Vol 7 (5) ◽  
pp. 1244-1252 ◽  
Author(s):  
David R. Glowacki ◽  
Emanuele Paci ◽  
Dmitrii V. Shalashilin
Keyword(s):  
Molecular Dynamics ◽  
Master Equation ◽  
Time Scales

Coarse Master Equation from Bayesian Analysis of Replica Molecular Dynamics Simulations†

2005 ◽  
Vol 109 (14) ◽  
pp. 6479-6484 ◽  
Author(s):  
Saravanapriyan Sriraman ◽  
Ioannis G. Kevrekidis ◽  
Gerhard Hummer
Keyword(s):  
Molecular Dynamics ◽  
Bayesian Analysis ◽  
Master Equation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

scholarly journals Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls

2010 ◽  
Vol 6 (6) ◽  
pp. 1798-1804 ◽  
Author(s):  
Joseph A. Morrone ◽  
Ruhong Zhou ◽  
B. J. Berne
Keyword(s):  
Molecular Dynamics ◽  
Time Scales ◽  
Multiple Time Scales ◽  
Multiple Time

An Integrated Molecular Dynamics and Monte Carlo Approach to Study Epitaxial Deposition of Silicon

2001 ◽  
Vol 672 ◽  
Author(s):  
Sweta Somasi ◽  
Bamin Khomami ◽  
Ronald Lovett
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Time Scales ◽  
Atomistic Simulation ◽  
Effective Coverage ◽  
Monte Carlo Approach ◽  
Epitaxial Deposition

ABSTRACTThe length and time scales of an atomistic simulation are often too small for any direct comparison with experimental observations. In order to study the coverage of pits (COPs) found on the Si (100) surface by epitaxial deposition, we first calculate rate of individual steps using molecular dynamics and then define a sequence of Monte-Carlo steps to study the effect of various factors on effective coverage of COPs.

scholarly journals Sorption, Structure and Dynamics of CO2 and Ethane in Silicalite at High Pressure: A Combined Monte Carlo and Molecular Dynamics Simulation Study

Molecules ◽  
2018 ◽  
Vol 24 (1) ◽  
pp. 99 ◽  
Author(s):  
Siddharth Gautam ◽  
Tingting Liu ◽  
David Cole
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Time Scales ◽  
Rotational Motion ◽  
High Pressures ◽  
Sorption Isotherms ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Structure And Dynamics ◽  
Low Pressures

Silicalite is an important nanoporous material that finds applications in several industries, including gas separation and catalysis. While the sorption, structure, and dynamics of several molecules confined in the pores of silicalite have been reported, most of these studies have been restricted to low pressures. Here we report a comparative study of sorption, structure, and dynamics of CO2 and ethane in silicalite at high pressures (up to 100 bar) using a combination of Monte Carlo (MC) and molecular dynamics (MD) simulations. The behavior of the two fluids is studied in terms of the simulated sorption isotherms, the positional and orientational distribution of sorbed molecules in silicalite, and their translational diffusion, vibrational spectra, and rotational motion. Both CO2 and ethane are found to exhibit orientational ordering in silicalite pores; however, at high pressures, while CO2 prefers to reside in the channel intersections, ethane molecules reside mostly in the sinusoidal channels. While CO2 exhibits a higher self-diffusion coefficient than ethane at low pressures, at high pressures, it becomes slower than ethane. Both CO2 and ethane exhibit rotational motion at two time scales. At both time scales, the rotational motion of ethane is faster. The differences observed here in the behavior of CO2 and ethane in silicalite pores can be seen as a consequence of an interplay of the kinetic diameter of the two molecules and the quadrupole moment of CO2.

scholarly journals Sequential Diffusion Spectra as a Tool for Studying Time-Dependent Translational Molecular Dynamics: A Cement Hydration Study

Molecules ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 68
Author(s):  
Igor Serša
Keyword(s):  
Molecular Dynamics ◽  
Porous Structure ◽  
Time Scales ◽  
Cement Hydration ◽  
Pulse Sequence ◽  
Spin Echo ◽  
Model Parameters ◽  
Signal Attenuation ◽  
Wide Range ◽  
Novel Method

The translational molecular dynamics in porous materials are affected by the presence of the porous structure that presents an obstacle for diffusing molecules in longer time scales, but not as much in shorter time scales. The characteristic time scales have equivalent frequency ranges of molecular dynamics, where longer time scales correspond to lower frequencies while the shorter time scales correspond to higher frequencies of molecular dynamics. In this study, a novel method for direct measurement of diffusion at a given frequency of translational molecular dynamics is exploited to measure the diffusion spectra, i.e., distribution of diffusion in a wide range of frequencies. This method utilizes NMR modulated gradient spin-echo (MGSE) pulse sequence to measure the signal attenuation during the train of spin-echoes formed in the presence of a constant gradient. From attenuation, the diffusion coefficient at the frequency equal to the inverse double inter-echo time is calculated. The method was employed to study the white cement hydration process by the sequential acquisition of the diffusion spectra. The measured spectra were also analyzed by the diffusion spectra model to obtain the time-dependence of the best-fit model parameters. The presented method can also be applied to study other similar systems with the time evolution of porous structure.

Molecular dynamics algorithm for multiple time scales: Systems with long range forces

1991 ◽  
Vol 94 (10) ◽  
pp. 6811-6815 ◽  
Author(s):  
Mark E. Tuckerman ◽  
Bruce J. Berne ◽  
Glenn J. Martyna
Keyword(s):  
Molecular Dynamics ◽  
Long Range ◽  
Time Scales ◽  
Multiple Time Scales ◽  
Multiple Time
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