Uncertainties of Thermal Conductivities From Equilibrium Molecular Dynamics Simulations

2016 ◽  
Author(s):  
Zuyuan Wang ◽  
Xiulin Ruan
Keyword(s):  
Molecular Dynamics ◽  
Correlation Time ◽  
Domain Size ◽  
Material System ◽  
Dynamics Simulations ◽  
Increasing Temperature ◽  
Solid Argon ◽  
Simulation Parameters ◽  
Simulation Time ◽  
Thermal Conductivities

The Green-Kubo method in the framework of equilibrium molecular dynamics (EMD) simulations is an effective method that has been widely used to calculate thermal conductivities of materials. The previous studies focused on the thermal conductivity values or the average values from repetitive simulations. Little research has been done to investigate the uncertainties of the thermal conductivities from EMD simulations. In this paper, we use solid argon as the material system to study the factors influencing the uncertainties of the predicted thermal conductivities. We find that the uncertainties decrease with the total simulation time as (ttotal)−α and increase with correlation time as (tcorre)β, where 0.48 < α, β < 0.52. We also find that the uncertainties decrease with increasing temperature, but the simulation domain size has a negligible effect. We propose some guidelines for selecting appropriate simulation parameters (e.g., the correlation time and total simulation time) to achieve a desired level of uncertainty. This work is potentially useful for future studies on calculating the thermal conductivities of materials using EMD simulations.

Molecular Dynamics Simulations of Polypropylene and Talcum Nanocomposite

2012 ◽  
Vol 466-467 ◽  
pp. 161-164
Author(s):  
Na Song ◽  
Qing Wang ◽  
Xiao Ji Zhang ◽  
Peng Ding
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Binding Energy ◽  
Potential Energy ◽  
Total Energy ◽  
Polymer Chains ◽  
Nanocomposite System ◽  
Modeling Techniques ◽  
Dynamics Simulations ◽  
Simulation Time

Molecular modeling techniques were applied to predicting binding energy for PP/talc and PP-MAH/talc. A supercell containing talc and two polymer chains of 25 repeating units length was constructed. The COMPASS forcefield has been used to represent the interactions in the nanocomposite system. The interactions are improved between the polymer and the clay in the presence of functional groups. And the total energy and potential energy between PP and the talc decreases almost linearly with the simulation time.

scholarly journals Molecular Dynamics Simulation of VEGFR2 with Sorafenib and Other Urea-Substituted Aryloxy Compounds

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Fancui Meng
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Md Simulation ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Dynamics Simulations ◽  
Simulation Time ◽  
Dynamics Method

The binding mode of sorafenib with VEGFR2 was studied using molecular docking and molecular dynamics method. The docking results show that sorafenib forms hydrogen bonds with Asp1046, Cys919, and Glu885 of VEGFR2 receptor. Molecular dynamics simulation suggests that the hydrogen bond involving Asp1046 is the most stable one, and it is almost preserved during all the MD simulation time. The hydrogen bond formed with Cys919 occurs frequently after 6 ns, while the bifurcated hydrogen bonds involving Glu885 occurs occasionally. Meantime, molecular dynamics simulations of VEGFR2 with 11 other urea-substituted aryloxy compounds have also been performed, and the results indicate that a potent VEGFR2 inhibitor should have lower interaction energy with VEGFR2 and create at least 2 hydrogen bonds with VEGFR2.

scholarly journals The impact of curcumin derived polyphenols on the structure and flexibility COVID-19 main protease binding pocket: a molecular dynamics simulation study

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11590
Author(s):  
Aweke Mulu ◽  
Mulugeta Gajaa ◽  
Haregewoin Bezu Woldekidan ◽  
Jerusalem Fekadu W/mariam
Keyword(s):  
Molecular Dynamics ◽  
Binding Affinity ◽  
Binding Pocket ◽  
Dynamics Simulation ◽  
World Health ◽  
Main Protease ◽  
Health Organization ◽  
Dynamics Simulations ◽  
Simulation Parameters ◽  
The Impact

The newly occurred SARS-CoV-2 caused a leading pandemic of coronavirus disease (COVID-19). Up to now it has infected more than one hundred sixty million and killed more than three million people according to 14 May 2021 World Health Organization report. So far, different types of studies have been conducted to develop an anti-viral drug for COVID-19 with no success yet. As part of this, silico were studied to discover and introduce COVID-19 antiviral drugs and results showed that protease inhibitors could be very effective in controlling. This study aims to investigate the binding affinity of three curcumin derived polyphenols against COVID-19 the main protease (Mpro), binding pocket, and identification of important residues for interaction. In this study, molecular modeling, auto-dock coupled with molecular dynamics simulations were performed to analyze the conformational, and stability of COVID-19 binding pocket with diferuloylmethane, demethoxycurcumin, and bisdemethoxycurcumin. All three compounds have shown binding affinity −39, −89 and −169.7, respectively. Demethoxycurcumin and bisdemethoxycurcumin showed an optimum binding affinity with target molecule and these could be one of potential ligands for COVID-19 therapy. And also, COVID-19 main protease binding pocket binds with the interface region by one hydrogen bond. Moreover, the MD simulation parameters indicated that demethoxycurcumin and bisdemethoxycurcumin were stable during the simulation run. These findings can be used as a baseline to develop therapeutics with curcumin derived polyphenols against COVID-19.

Modern Status Of Researches Of Nanofluids Viscosity

2015 ◽  
Vol 10 (1) ◽  
pp. 5-22
Author(s):  
Valeriy Rudyak
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Fluid Model ◽  
Relative Viscosity ◽  
Viscosity Coefficient ◽  
Viscosity Coefficients ◽  
Nanoparticles Concentration ◽  
Nanofluid Viscosity ◽  
Dynamics Simulations ◽  
Increasing Temperature

In present paper the regular review of researches of nanofluids viscosity is made. Known experimental data and data of molecular dynamic simulation are considered. It is shown, that nanofluid viscosity is not described by the classical theories. All experimental data and molecular dynamics simulations suggest that at a fixed volume concentration of nanoparticles, the nanofluid viscosity is significantly higher than the viscosity of conventional suspensions. Generally it depends not only on concentration наночастиц, but also from their size. The viscosity coefficients increase with decreasing nanoparticle size. It was shown by molecular dynamics method that the viscosity coefficient of nanofluid depends on the nanoparticles material. At low and moderate concentrations of nanoparticles, the relative viscosity coefficient does not change with increasing temperature. In this case the temperature dependence of nanofluid viscosity is determined by the corresponding dependence of based fluid. The nanofluid prepared on distilled water with CuO nanoparticles has the nonNewtonian rheology if the concentration of the particles is more than 0.25 in the volume. It was established that their rheology is well described by the power law fluid model. With an increase in concentration of nanoparticles, nanofluid index decreases, but the consistency parameter K, on the contrary, increases. The correlation defining dependence of the viscosity coefficient on nanoparticles concentration and their size is offered. The reasons of nonclassical behavior of nanofluids are in detail discussed.

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