Improving Monte-Carlo and Molecular Dynamics Simulation Outcomes Using Temperature-Dependent Interaction Parameters: The Case of Pure LJ Fluid

2015 ◽  
Vol 12 (02) ◽  
pp. 1550003 ◽  
Author(s):  
Ali Kh. Al-Matar ◽  
Ahmed H. Tobgy ◽  
Ibrahim A. Suleiman ◽  
Majdi A. Al-Faiad
Keyword(s):  
Molecular Dynamics ◽  
Mean Square Displacement ◽  
Dynamics Simulation ◽  
Interaction Parameters ◽  
Mean Square ◽  
Temperature Dependent ◽  
Temperature Range ◽  
Significant Difference ◽  
Dependent Interaction ◽  
Vapor Liquid

The main proposition of this work is that introducing temperature-dependent interaction parameters (TDIP) instead of using temperature-independent interaction parameters (TIIP) may lead to improvement in the prediction of phase equilibrium properties such as vapor liquid equilibria, and transport properties e.g., self-diffusivity. Published second virial coefficient data was used to fit a simple two parameter temperature-dependent model for the collision diameter and well depth. This fitting procedure reduces the Root Mean Square Deviation (RMSD) between the experimental and predicted second virial coefficients by tenfold compared to the best TIIP and by 15 fold with the literature values. The vapor–liquid coexistence curve for argon was simulated in the NVT Gibbs ensemble in the temperature range: 110–148 K. The critical temperature and density were determined using the Ising-scaling model. The TDIP simulations produce, in general, a more accurate phase diagram compared to the diagram generated using TIIP. RMSD is reduced by 42.1% using TDIP. Also, there was no significant difference between the results obtained using TDIP and the highly accurate and computationally demanding phase diagrams based on three body contributions implementing Axillrod–Teller correction. Self-diffusivities of atomic argon were evaluated using the mean square displacement or the Einstein method using equilibrium molecular dynamics (MD) at a pressure of 13 bars and a temperature range from 90 K up to 135 K in the isobaric, isothermal NPT ensemble. TDIP, in general, produces more accurate self-diffusivities than the values computed by TIIP simulations. RMSD is reduced by about 64% using the temperature-dependent parameters.

Molecular dynamics simulation of aggregation of monocrystal and polycrystal copper nanoparticles

2019 ◽  
Vol 33 (16) ◽  
pp. 1950168
Author(s):  
Linxing Zhang ◽  
Guang Hong ◽  
Shouyin Cai
Keyword(s):  
Molecular Dynamics ◽  
Lattice Structure ◽  
Displacement Vector ◽  
Mean Square Displacement ◽  
Dynamics Simulation ◽  
Gyration Radius ◽  
Mean Square ◽  
Shrinkage Ratio ◽  
Lower Temperature ◽  
Dynamics Simulations

Molecular dynamics simulations were employed to investigate the aggregation of monocrystal and polycrystal nanoparticles. The lattice structure, displacement vector, potential energy, shrinkage ratio, relative gyration radius and mean square displacement of the two systems are compared. The results indicate that the aggregation of polycrystal nanoparticles is more drastic than that of monocrystal nanoparticles. Besides, the polycrystal nanoparticles are found contacted and melted at lower-temperature than that of monocrystal nanoparticles. The reason for all these phenomena is that there is additional surface energy in the grain boundary of polycrystal nanoparticles.

scholarly journals The Vapor-Liquid Phase Diagram of Pure Methane Using Temperature-Dependent Interaction Parameters: A Monte Carlo Simulation

2019 ◽  
Vol 2 (1) ◽  
pp. 1-6
Author(s):  
Ibrahim Suleiman
Keyword(s):  
Phase Diagram ◽  
Monte Carlo ◽  
Liquid Phase ◽  
Critical Density ◽  
Second Virial Coefficient ◽  
Interaction Parameters ◽  
Temperature Dependent ◽  
Temperature Dependent Model ◽  
Dependent Interaction ◽  
Vapor Liquid

Adopting temperature-dependent interaction parameters in the Lennard-Jones potential, the vapor-liquid phase diagram of methane was produced using NVT Gibbs Ensemble Monte Carlo technique. Published second virial coefficient data were used to fit a simple two-parameter temperature-dependent model for the interaction parameters. The simulations were carried out in the temperature range 120-190 K. The critical density and temperature were evaluated using Ising-scaling model. Using the temperature-dependent interaction parameters in the simulation has reduced the root mean square deviation by 94.7% compared to the temperature-independent interaction parameters. The evaluated critical temperature was enhanced using temperature-dependent interaction parameters, whereas the simulations using temperature-independent interaction parameters predict a better critical density value

The molecular dynamics simulation on the mechanical properties of Ni glass with external pressure

2017 ◽  
Vol 31 (20) ◽  
pp. 1750138 ◽  
Author(s):  
Chuan-Hui Zhang ◽  
Ying Wang ◽  
Dong-Bai Sun
Keyword(s):  
Molecular Dynamics ◽  
Mean Square Displacement ◽  
External Pressure ◽  
Rapid Quenching ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Mean Square ◽  
External Pressures ◽  
Ratio Rule ◽  
Pair Distribution Functions

In this paper, rapid quenching of Ni from crystal to metallic glass (MG) at different external pressures is simulated by molecular dynamics. The pair distribution functions (PDFs), mean-square displacement, glass transition temperature ([Formula: see text]) and elastic property are calculated and compared with each other. The split of the second PDF peak means the liquid’s transition to glass state starts as previously reported for other MGs. And the [Formula: see text] ratio rule is found to hold very well in Ni MG and reveals the SPO structural feature in the configurations. Moreover, with high external pressure, [Formula: see text] values are more approximated by density–temperature and enthalpy–temperature curves. At last, the elastic modulus and mechanics modulus of quenching models produced a monotonous effect with increasing external pressure and temperature.

scholarly journals Tentative Peptide‒Lipid Bilayer Models Elucidating Molecular Behaviors and Interactions Driving Passive Cellular Uptake of Collagen-Derived Small Peptides

Molecules ◽  
2021 ◽  
Vol 26 (3) ◽  
pp. 710
Author(s):  
Pathomwat Wongrattanakamon ◽  
Wipawadee Yooin ◽  
Busaban Sirithunyalug ◽  
Piyarat Nimmanpipug ◽  
Supat Jiranusornkul
Keyword(s):  
Lipid Bilayer ◽  
Lipid Bilayers ◽  
Mean Square Displacement ◽  
Dynamics Simulation ◽  
Coordinate Frame ◽  
Mean Square ◽  
Binding Modes ◽  
Small Peptides ◽  
Collagen Peptides ◽  
Electron Density Profiles

Collagen contains hydroxyproline (Hyp), which is a unique amino acid. Three collagen-derived small peptides (Gly-Pro-Hyp, Pro-Hyp, and Gly-Hyp) interacting across a lipid bilayer (POPC model membrane) for cellular uptakes of these collagen-derived small peptides were studied using accelerated molecular dynamics simulation. The ligands were investigated for their binding modes, hydrogen bonds in each coordinate frame, and mean square displacement (MSD) in the Z direction. The lipid bilayers were evaluated for mass and electron density profiles of the lipid molecules, surface area of the head groups, and root mean square deviation (RMSD). The simulation results show that hydrogen bonding between the small collagen peptides and plasma membrane plays a significant role in their internalization. The translocation of the small collagen peptides across the cell membranes was shown. Pro-Hyp laterally condensed the membrane, resulting in an increase in the bilayer thickness and rigidity. Perception regarding molecular behaviors of collagen-derived peptides within the cell membrane, including their interactions, provides the novel design of specific bioactive collagen peptides for their applications.

Molecular Dynamics Study of Microscopic Mechanism of Diffusion in Li2SiO3 System

1991 ◽  
Vol 46 (7) ◽  
pp. 616-620 ◽  
Author(s):  
Junko Habasaki
Keyword(s):  
Molecular Dynamics ◽  
Coordination Number ◽  
Md Simulation ◽  
Mean Square Displacement ◽  
Mean Square ◽  
Lithium Ions ◽  
Microscopic Mechanism ◽  
Trapping Model ◽  
The Mean

MD simulation has been performed to learn the microscopic mechanism of diffusion of ions in the Li2SiO3 system. The motion of lithium ions can be explained by the trapping model, where lithium is trapped in the polyhedron and moves with fluctuation of the coordination number. The mean square displacement of lithium was found to correlate well with the net changes in coordination number.

scholarly journals Effects of the Temperature and the pH on the Main Protease of SARS-CoV-2: A Molecular Dynamics Simulation Study

2021 ◽  
Vol 12 (6) ◽  
pp. 7239-7248
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Root Mean Square ◽  
Dynamics Simulation ◽  
Effect Of Temperature ◽  
Water Molecules ◽  
Mean Square ◽  
Main Protease ◽  
Decreasing Ph ◽  
Increasing Temperature

The novel coronavirus, recognized as COVID-19, is the cause of an infection outbreak in December 2019. The effect of temperature and pH changes on the main protease of SARS-CoV-2 were investigated using all-atom molecular dynamics simulation. The obtained results from the root mean square deviation (RMSD) and root mean square fluctuations (RMSF) analyses showed that at a constant temperature of 25℃ and pH=5, the conformational change of the main protease is more significant than that of pH=6 and 7. Also, by increasing temperature from 25℃ to 55℃ at constant pH=7, a remarkable change in protein structure was observed. The radial probability of water molecules around the main protease was decreased by increasing temperature and decreasing pH. The weakening of the binding energy between the main protease and water molecules due to the increasing temperature and decreasing pH has reduced the number of hydrogen bonds between the main protease and water molecules. Finding conditions that alter the conformation of the main protease could be fundamental because this change could affect the virus’s functionality and its ability to impose illness.

scholarly journals Emulsification of Surfactant on Oil Droplets by Molecular Dynamics Simulation

Molecules ◽  
2020 ◽  
Vol 25 (13) ◽  
pp. 3008
Author(s):  
Yaoshuang Cheng ◽  
Shiling Yuan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Heavy Oil ◽  
Molecular Level ◽  
Sodium Dodecyl ◽  
Mean Square Displacement ◽  
Dynamics Simulation ◽  
Oil Droplets ◽  
Hydration Layer ◽  
Oil Droplet

Heavy oil in crude oil flooding is extremely difficult to extract due to its high viscosity and poor fluidity. In this paper, molecular dynamics simulation was used to study the emulsification behavior of sodium dodecyl sulfonate (SDSn) micelles on heavy oil droplets composed of asphaltenes (ASP) at the molecular level. Some analyzed techniques were used including root mean square displacement, hydrophile-hydrophobic area of an oil droplet, potential of mean force, and the number of hydrogen bonds between oil droplet and water phase. The simulated results showed that the asphaltene with carboxylate groups significantly enhances the hydration layer on the surface of oil droplets, and SDSn molecules can change the strength of the hydration layer around the surface of the oil droplets. The water bridge structure between both polar heads of the surfactant was commonly formed around the hydration layer of the emulsified oil droplet. During the emulsification of heavy oil, the ratio of hydrophilic hydrophobic surface area around an oil droplet is essential. Molecular dynamics method can be considered as a helpful tool for experimental techniques at the molecular level.

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