Molecular dynamics simulation of single ions in aqueous solutions: effects of the flexibility of the water molecules

1990 ◽  
Vol 94 (15) ◽  
pp. 6049-6055 ◽  
Author(s):  
E. Guardia ◽  
J. A. Padro
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Dynamics Simulation ◽  
Water Molecules

Molecular Dynamics Simulation of the Aggregation Patterns in Aqueous Solutions of Bile Salts at Physiological Conditions

2015 ◽  
Vol 119 (51) ◽  
pp. 15631-15643 ◽  
Author(s):  
Fatmegyul Mustan ◽  
Anela Ivanova ◽  
Galia Madjarova ◽  
Slavka Tcholakova ◽  
Nikolai Denkov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Bile Salts ◽  
Dynamics Simulation ◽  
Physiological Conditions

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.

Structures of Cationic and Anionic Polyelectrolytes in Aqueous Solutions: The Sign Effect

Soft Matter ◽  
2022 ◽  
Author(s):  
Chengjiang Lin ◽  
Hao Wei ◽  
Hongfei Li ◽  
Xiaozheng Duan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Dynamics Simulation ◽  
Solvation Effects ◽  
Cationic Polyelectrolytes ◽  
Sign Effect

In this study, we use molecular dynamics simulation to explore the structures of anionic and cationic polyelectrolytes in aqueous solutions. We first confirm the significantly stronger solvation effects of single...

Molecular dynamics simulation of homogeneous nucleation of supersaturated potassium chloride (KCl) in aqueous solutions

CrystEngComm ◽  
2019 ◽  
Vol 21 (48) ◽  
pp. 7507-7518 ◽  
Author(s):  
Soroush Ahmadi ◽  
Yuanyi Wu ◽  
Sohrab Rohani
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Potassium Chloride ◽  
Homogeneous Nucleation ◽  
Md Simulation ◽  
Crystal Nucleation ◽  
Dynamics Simulation

Molecular dynamics (MD) simulation is used to investigate the mechanism of crystal nucleation of potassium chloride (KCl) in a supersaturated aqueous solution at 293 K and 1 atm.

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