The Effect of Temperature and Solvent Concentration on the Nanomotor Motion by Molecular Dynamics Simulation

2012 ◽  
Vol 190-191 ◽  
pp. 253-256
Author(s):  
Guang Yu Zhang ◽  
Qian Sun ◽  
Long Qiu Li ◽  
Lin Wang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Low Temperature ◽  
Mass Velocity ◽  
Center Of Mass ◽  
Dynamics Simulation ◽  
Effect Of Temperature ◽  
Kinematics Analysis ◽  
Solvent Concentration ◽  
Maximum Value

Nanomotors are nanoscale devices capable of converting energy into movement and forces. In this work, a molecular dynamic model based on a chemically powered nanomotor is established. Based on molecular dynamics, dynamics and kinematics analysis have been made, and the motion of the model has been simulated. Finally, we get the effect of the temperature and the solvent concentration on the nanomotor motion respectively. The center-of-mass velocity of the nanomotor along its axis increases roughly linearly with low temperature, and then gradually reaches a maximum value. The center-of-mass velocity of the nanomotor along its axis increases roughly linearly with low solvent concentration, and then gradually reaches a maximum value.

Momentum Removal to Obtain the Position-Dependent Diffusion Constant in Constrained Molecular Dynamics Simulation

2021 ◽  
Author(s):  
Kazushi Fujimoto ◽  
Tetsuro Nagai ◽  
Tsuyoshi Yamaguchi
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Mass Velocity ◽  
Center Of Mass ◽  
Heterogeneous Systems ◽  
Diffusion Constant ◽  
Dynamics Simulation ◽  
Coulombic Interaction ◽  
Ewald Method ◽  
Theoretical Predictions

<div>The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink-Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate the period of the removal of the center-of-mass velocity in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf-Roux method.</div>

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.

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.

Determination of ion quantity by using low-temperature ion density theory and molecular dynamics simulation

2015 ◽  
Vol 24 (11) ◽  
pp. 113703 ◽  
Author(s):  
Li-Jun Du ◽  
Hong-Fang Song ◽  
Hai-Xia Li ◽  
Shao-Long Chen ◽  
Ting Chen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Low Temperature ◽  
Dynamics Simulation ◽  
Ion Density
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