Structural Order of Water Molecules around the Polyrotaxane including PEG, α-Cyclodextrin, and Linker α -Lipoic acid onto Gold surface by Molecular Dynamics Simulation.

2021 ◽  
Author(s):  
Tue Minh Nhu Le ◽  
Le Van Sang ◽  
Hitoshi Washizu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Lipoic Acid ◽  
Materials Science ◽  
Molecular Level ◽  
Gold Surface ◽  
Dynamics Simulation ◽  
Molecular Water ◽  
Water Molecules ◽  
Structural Order

In materials science, water plays an important part, especially at the molecular level. It shows various properties when sorbed onto surfaces of polymers. The structure of the molecular water ensemble...

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-level insight of hindered phenol AO-70/nitrile-butadiene rubber damping composites through a combination of a molecular dynamics simulation and experimental method

RSC Advances ◽  
2016 ◽  
Vol 6 (89) ◽  
pp. 85994-86005 ◽  
Author(s):  
Xiuying Zhao ◽  
Geng Zhang ◽  
Feng Lu ◽  
Liqun Zhang ◽  
Sizhu Wu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Experimental Method ◽  
Molecular Level ◽  
Dynamics Simulation ◽  
Butadiene Rubber ◽  
Damping Properties ◽  
Nitrile Butadiene Rubber ◽  
Hindered Phenol

The damping properties of AO-70/NBR composites get a noteworthy increase with the introduction of AO-70—max tan δincreased by 66.9%.

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.

Multiscale flow characteristics of droplet spreading with microgravity conditions

2019 ◽  
Vol 97 (8) ◽  
pp. 869-874
Author(s):  
Xue-Qing Chen ◽  
Lei Tong
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Solid Wall ◽  
Gold Surface ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Contact Radius ◽  
Droplet Spreading ◽  
Fast Spreading ◽  
Slow Spreading

In this paper, mesoscopic lattice–Boltzmann method (LBM) and microscopic molecular dynamics simulation method were used to simulate droplet dynamic wetting under microgravity. In terms of LBM, the wetting process of a droplet on a solid wall surface was simulated by introducing the fluid–fluid and solid–fluid interactions. In terms of molecular dynamics simulation, the spreading process of water on gold surface was simulated. Calculation results showed that two kinds of calculation methods were based on the microscopic molecular theory or mesoscopic kinetics theory, and such models could effectively overcome the contact line paradox issue, which results from the macro-continuum assumption and non-slip boundary condition assumption. The spreading exhibits two-stage behavior: fast spreading and slow spreading stages. For the two simulation methods, the ratio of fast spreading stage duration to slow spreading duration, spreading capacity (equilibrium contact radius/initial radius), and the spreading exponent of the rapid stage were very close. However, the predictive spreading index of the slow spreading stage was different, owing to the different spreading mechanisms between meso- and nanoscales.

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