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>

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>

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.

Molecular Dynamics Simulation Study of the Effect of Ni, Fe, Cu on Cryolite Molten Salt System 78% Na3AlF6-9.5%AlF3-5.0%CaF2-7.5%-Al2O3

2021 ◽  
Vol 1026 ◽  
pp. 39-48
Author(s):  
Han Bing He ◽  
Yu Si Wang ◽  
Ze Xiang Luo ◽  
Jing Zeng
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molten Salt ◽  
Diffusion Mechanism ◽  
Research Work ◽  
Dynamics Simulation ◽  
Salt System ◽  
Electrolyte System ◽  
Aluminum Composite ◽  
Molten Salt System

The effect of different additives Ni, Fe, Cu on the structure and properties of electrolyte system 78% Na3AlF6- -9.5%AlF3-5.0%CaF2-7.5%Al2O3 at 1200K and 1.01Mpa was studied by molecular dynamics method. The radial distribution function, coordination number, diffusion coefficient, conductivity, and viscosity of the system were discussed in detail. The results demonstrated that the order of the self-diffusion coefficient of ions in the electrolyte system is: Na+ > F- > O2- > Ca2+ >Al3+. The addition of Ni and Fe connected the free aluminum composite ion groups in the system through fluorine bridges, which enhanced the interaction between Al3+ and Al3+. The addition of Cu weakened the interaction between Al3 + and Al3+ and the F-. The interaction between Al3+ and Na+, [AlF7]4- ionic groups might appeared in the melt system. After adding NiO, Fe2O3, and Cu, the electrical conductivity of the system increased, and the viscosity decreased. The research work revealed the influence of Ni, Fe, Cu on the ion existence form, mobility, inter-ion interaction and diffusion mechanism of cryolite molten salt system, which has important guiding significance for aluminum electrolysis production.

scholarly journals Molecular Dynamics Simulation of Zener Pinning by Differently Shaped and Oriented Particles

2021 ◽  
Vol 8 ◽  
Author(s):  
Yi Li ◽  
Jian Zhou ◽  
Runjie Li ◽  
Qingyu Zhang
Keyword(s):  
Molecular Dynamics ◽  
Dynamics Simulation ◽  
Pinning Force ◽  
Theoretical Studies ◽  
Constant Energy ◽  
Zener Pinning ◽  
Interaction Processes ◽  
Interface Characteristics ◽  
Theoretical Predictions ◽  
Ag Particle

Zener pinning between a curved Cu grain boundary (GB) and a differently shaped and oriented Ag particle has been simulated via molecular dynamics. The computed magnitudes of the maximum pinning force agreed with theoretical predictions only when the force was small. As the force increased, discrepancy became obvious. Through careful inspection of the structures of the Cu–Ag interfaces, detailed interaction processes, and variation of the Cu GB during the interaction, the discrepancy is found to correlate with GB faceting, which very likely reduces the maximum pinning force and facilitates boundary passage. GB anisotropy and/or interface characteristics are also found to slightly contribute to the discrepancy. These findings suggest that the assumption of an isotropic GB with constant energy utilized in previous theoretical studies for deriving the maximum pinning force might be inappropriate and that an accurate maximum pinning force could not be predicted without knowing the effects of GB evolution together with detailed properties of both GBs and interfaces.

scholarly journals Molecular Dynamics Simulation of Wetting Behavior: Contact Angle Dependency on Water Potential Models

2021 ◽  
Vol 1 (1) ◽  
pp. 10
Author(s):  
Lukman Hakim ◽  
Irsandi Dwi Oka Kurniawan ◽  
Ellya Indahyanti ◽  
Irwansyah Putra Pradana
Keyword(s):  
Molecular Dynamics ◽  
Contact Angle ◽  
Liquid Droplet ◽  
Center Of Mass ◽  
Contact Angles ◽  
Surface Wettability ◽  
Dynamics Simulation ◽  
Potential Models ◽  
Surface Hydrophilicity ◽  
Dynamics Simulations

The underlying principle of surface wettability has obtained great attentions for the development of novel functional surfaces. Molecular dynamics simulations has been widely utilized to obtain molecular-level details of surface wettability that is commonly quantified in term of contact angle of a liquid droplet on the surface. In this work, the sensitivity of contact angle calculation at various degrees of surface hydrophilicity to the adopted potential models of water: SPC/E, TIP4P, and TIP5P, is investigated. The simulation cell consists of a water droplet on a structureless surface whose hydrophilicity is modified by introducing a scaling factor to the water-surface interaction parameter. The simulation shows that the differences in contact angle described by the potential models are systematic and become more visible with the increase of the surface hydrophilicity. An alternative method to compute a contact angle based on the height of center-of-mass of the droplet is also evaluated, and the resulting contact angles are generally larger than those determined from the liquid-gas interfacial line.

scholarly journals Atomic-Scale Mechanism Investigation of Mass Transfer in Laser Fabrication Process of Ti-Al Alloy via Molecular Dynamics Simulation

Metals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1660
Author(s):  
Ziqi Cui ◽  
Xianglin Zhou ◽  
Qingbo Meng
Keyword(s):  
Molecular Dynamics ◽  
Mass Transfer ◽  
Diffusion Coefficient ◽  
Particle System ◽  
Fabrication Process ◽  
Atomic Scale ◽  
Dynamics Simulation ◽  
Al Alloy ◽  
Laser Fabrication ◽  
Solute Atoms

This article deals with a Ti-Al alloy system. Molecular dynamics simulation was used to simulate and explore the mass transfer behavior during the laser fabrication process at atomic scale. The research goal is to investigate the mass transfer mechanism at atomic scale and the movement of solute atoms during the laser fabrication process. The mean square displacement (MSD), radial distribution function (RDF), atomic number density, and atomic displacement vector were calculated to characterize it. The results show that the TiAl alloy is completely melted when heated up to 2400 K, and increasing the temperature past 2400 K has little effect on mass transfer. As the heating time increases, the diffusion coefficient gradually decreases, the diffusion weakens, and the mass transfer process gradually stabilizes. In Ti-Al binary alloys, the diffusion coefficients of different solute atoms are related to the atomic fraction. During the melting process, the alloy particle system has a greater diffusion coefficient than the elemental particle system.

Molecular Dynamics Simulation of Homogeneous and Heterogeneous Thermal Bubble Nucleation

2011 ◽  
Author(s):  
Min Chen ◽  
Yunfei Chen ◽  
Juekuan Yang ◽  
Yandong Gao ◽  
Deyu Li
Keyword(s):  
Molecular Dynamics ◽  
Heterogeneous Systems ◽  
Liquid Argon ◽  
Bubble Nucleation ◽  
Dynamics Simulation ◽  
Nucleation Temperature ◽  
The Common ◽  
Solid Walls ◽  
Common Understanding ◽  
Superheat Limit

Thermal bubble nucleation was studied using molecular dynamics for both homogeneous and heterogeneous systems using isothermal-isobaric (NPT) and isothermal-isostress (NPzzT) ensembles. Simulation results indicate that homogeneous thermal bubble nucleation is induced from cavities occurring spontaneously in the liquid when the temperature exceeds the superheat limit. In contrast to published results using NVE and NVT ensembles, no stable nanoscale bubble exists in NPT ensembles, but instead, the whole system changes into vapor phase. For a heterogeneous system composed of a nanochannel with an initial distance of 3.49 nm between the two solid plates, it is found that if the liquid-solid interaction is equal to or stronger than that between liquid argon atoms, the bubble nucleation temperature of the confined liquid argon can be higher than the corresponding homogeneous nucleation temperature, because of the more ordered arrangement of atoms within two solid walls nanometers apart. This observation is in contradiction to the common understanding that homogeneous bubble nucleation temperature sets an upper limit for thermal phase change under a given pressure. Compared to the system where the liquid-solid interaction is the same as that between liquid argon atoms, the system with reduced liquid-solid interaction possesses a significantly reduced bubble nucleation temperature, while the system with enhanced liquid-solid interaction only has a marginally increased bubble nucleation temperature.

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