Molecular dynamics simulation to assess the effect of temperature on diffusion coefficients of different ions and water molecules in C-S-H

2017 ◽  
Vol 22 (4) ◽  
pp. 483-497 ◽  
Author(s):  
B. Zehtab ◽  
A. Tarighat
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Diffusion Coefficients ◽  
Dynamics Simulation ◽  
Effect Of Temperature ◽  
Water Molecules

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.

Molecular Dynamics Simulation on Aqueous Solution of Calcium Carbonate System

2019 ◽  
Vol 394 ◽  
pp. 73-78
Author(s):  
Da Fang Wang ◽  
Dong Dong Meng ◽  
Feng Jun Wang ◽  
Xin Dong Cui
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Diffusion Coefficients ◽  
Binding Energies ◽  
The Other ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Neutral Surface ◽  
Carbonate System

Molecular dynamics simulation was used to investigate two models of aqueous solution ofcalcium carbonate system between 283K and 373K. The diffusion coefficients of water moleculesdemonstrated that both the electropositive surface (110) on Model-I and neutral surface (104) onModel-II showed interaction with the water molecules, and the surface (110) exhibited strongerelectrostatic interaction with water molecules than the latter, besides obvious anomaly appeared near343K on Model-I. On the other hand, surface (110) exhibited anomalous influences on Ca2+ andCO32- ions near 313K and 343K on Model-I, and only a broad anomaly on CO32- ions near 343K onModel-II. The binding energies between surface (110) / (104) and Ca2+ /CO32- ions demonstrated thatthe surface (104)were more favorable for the growth of the new crystal but weak for the diffusion.

Effect of temperature on properties of aluminum/single-walled carbon nanotube nanocomposite by molecular dynamics simulation

2019 ◽  
Vol 234 (2) ◽  
pp. 635-642 ◽  
Author(s):  
Mohsen Motamedi ◽  
AH Naghdi ◽  
SK Jalali
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulation ◽  
Young’S Modulus ◽  
Young's Modulus ◽  
Strain Curve ◽  
Dynamics Simulation ◽  
Effect Of Temperature ◽  
Metal Composite

Composite materials have become popular because of high mechanical properties and lightweight. Aluminum/carbon nanotube is one of the most important metal composite. In this research, mechanical properties of aluminum/carbon nanotube composite were obtained using molecular dynamics simulation. Then, effect of temperature on stress–strain curve of composite was studied. The results showed by increasing temperature, the Young’s modulus of composite was decreased. More specifically increasing the temperature from 150 K to 620 K, decrease the Young’s modulus to 11.7%. The ultimate stress of composite also decreased by increasing the temperature. A continuum model of composite was presented using finite element method. The results showed the role of carbon nanotube on strengthening of composite.

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