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
2005 ◽  
Vol 109 (14) ◽  
pp. 6479-6484 ◽  
Author(s):  
Saravanapriyan Sriraman ◽  
Ioannis G. Kevrekidis ◽  
Gerhard Hummer

2010 ◽  
Vol 6 (6) ◽  
pp. 1798-1804 ◽  
Author(s):  
Joseph A. Morrone ◽  
Ruhong Zhou ◽  
B. J. Berne

2001 ◽  
Vol 672 ◽  
Author(s):  
Sweta Somasi ◽  
Bamin Khomami ◽  
Ronald Lovett

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.


Molecules ◽  
2018 ◽  
Vol 24 (1) ◽  
pp. 99 ◽  
Author(s):  
Siddharth Gautam ◽  
Tingting Liu ◽  
David Cole

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.


Molecules ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 68
Author(s):  
Igor Serša

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.


1991 ◽  
Vol 94 (10) ◽  
pp. 6811-6815 ◽  
Author(s):  
Mark E. Tuckerman ◽  
Bruce J. Berne ◽  
Glenn J. Martyna

Sign in / Sign up

Export Citation Format

Share Document