• Bulletin of the Korean Chemical Society
• /
• v.34 no.10
• /
• pp.2931-2936
• /
• 2013

This paper presents results for the calculation of transport properties of noble gases (He, Ne, Ar, Kr, and Xe) at 273.15 K and 1.00 atm using equilibrium molecular dynamics (EMD) simulations through a Lennard-Jones (LJ) intermolecular potential. We have utilized the revised Green-Kubo formulas for the stress (SAC) and the heat-flux auto-correlation (HFAC) functions to estimate the viscosities (${\eta}$) and thermal conductivities (${\lambda}$) of noble gases. The original Green-Kubo formula was employed for diffusion coefficients (D). The results for transport properties (D, ${\eta}$, and ${\lambda}$) of noble gases at 273.15 and 1.00 atm obtained from our EMD simulations are in a good agreement with the rigorous results of the kinetic theory and the experimental data. The radial distribution functions, mean square displacements, and velocity auto-correlation functions of noble gases are remarkably different from those of liquid argon at 94.4 K and 1.374 $g/cm^3$.

• Transactions of the Korean Society of Mechanical Engineers B
• /
• v.29 no.1 s.232
• /
• pp.159-168
• /
• 2005

In recent studies, it was reported that there existed the temperature discontinuity at a liquid-vapor interface in an equilibrium state. However, from the viewpoint of the classical thermodynamics, it is highly questionable result although considering that the experiments related with a boundary layer is very difficult due to the extremely thin thickness of it. To clarify whether the temperature discontinuity over a liquid-vapor interface really exists, the computer simulations were performed. From the simulation results, it could be concluded that the misconception in a temperature calculation might result in non-uniform temperature distributions over an interface under an equilibrium state.

• Bulletin of the Korean Chemical Society
• /
• v.21 no.4
• /
• pp.434-440
• /
• 2000

We present the results of computer simulation for the steady shear flows of rodlike molecules using nonequi-librium molecular dynamics simulation (NEMD) method. The model particle is a rigid rod composed of lin-early connected 6-sites and the Lennard-Jones 12-6 potential governs interactions between sites in different molecules. The system of rodlike molecules exhibits the change of orientational structure, that is, isotropic-nematic transition at high shear rates. We elucidate the nature of the ordered system developed from an isotro-pic phase by steady shear through an analysis of various quantities: orientational order parameters, orientational pair correlation functions, orientational distribution function, and snapshots of configurations. The effects of temperature and density on the shear rate dependence of orientational structure are described.

• Advances in nano research
• /
• v.15 no.2
• /
• pp.105-111
• /
• 2023

Integrin αvβ3 is one of the receptors expressed in cancer cells. RGD peptides have the potential to target integrin αvβ3 (receptor), which can increase drug delivery efficiency. In this study, 55 different RGD dimer motifs were investigated. At first, the binding energy between RGD peptides and the receptor was calculated using molecular docking. Then, three RGD peptides with the strongest binding energy with the receptor were selected, and their dynamic adsorption on the receptor was simulated by molecular dynamics (MD). The obtained results showed that a sequence that has RGD at the beginning and end with tryptophan (TRP) has strong Lennard-Jones (LJ) and electrostatic interactions with Integrin αvβ3 and has changed the conformation of receptor significantly, which analyzed by root mean square deviation (RMSD) and radius of gyration.

• Bulletin of the Korean Chemical Society
• /
• v.21 no.11
• /
• pp.1133-1137
• /
• 2000

Gibbs ensemble Monte Carlo simulations were performed to calculate the vapor- liquid coexistence properties for the binary mixtures $CO_2/C_3H8$, $CO_2/CH_3OCH_3$, and $CO_2/CH_3COCH_3.$ For all the molecules the potential between sites in different molecules was simply calculated by the Lennard-Jones potential. Density of the mixture, composition of the mixture, the pressure-composition diagram, the chemical potential of component, and the radial distribution function were calculated at vapor- liquid equilibrium. The composition and the density of both vapor and liquid from simulation agreed considerably well with the experimental values over a wide range of pressures. The radial distribution functions in the liquid mixtures showed that $CO_2$ molecules tended to form cluster with each other and $C_3H8$ molecules also aggregated each other due to the weak interaction between $CO_3$ and $C_3H8$ molecule. However the interaction potentials between the same components were similar to those between the different components in the liquid mixtures $CO_2/CH_3OCH_3$ and $CO_2/CH_3COCH_3$.

• Proceedings of the KSME Conference
• /
• 2008.11a
• /
• pp.1788-1793
• /
• 2008

Classical molecular dynamics simulations (MDS) were conducted to simulate nano-sized cluster collisions with a weakly attractive static surface. Energy exchanges associated with the cluster collision and the adhesion probability are discussed. Routes of the energy exchanges and the kinetic energy loss are vastly altered in their mode according to the cluster incident velocity. In the elastic collision regime ($V_0$<0.1), most incident kinetic energy is recovered into the rebounding kinetic energy, but a little loss in the incident kinetic energy causes the cluster adhesion. Dissipated kinetic energy is converted into the rotational energy. In the weakly plastic collision regime (0.1<$V_0$<0.3), the transition from elastic to plastic collision occurs, and a large part of the released potential energy is converted into rebounding translational energy. For strongly plastic collisions ($V_0$>0.3), permanent cluster deformation occurs with extensive collapse of the lattice structure inducing a solid-to-solid phase transition; moreover, most of the cluster kinetic energy is converted into cluster potential and thermal energy.

• Bulletin of the Korean Chemical Society
• /
• v.4 no.5
• /
• pp.223-227
• /
• 1983

A molecular dynamic computer experiment was performed on a system of 108 particles composed of a single polymer chain and solvent molecules. The state considered was in the immediate neighborhood of the triple point of the system. The polymer itself is an analog of a freely jointed chain. The Lennard-Jones potential was used to represent the interactions between all particles except for that between the chain elements forming a bond in the polymer chain, for which the interaction was expressed by a harmonic potential. The self-diffusion coefficient and velocity autocorrelation function (VACF) of a polymer were calculated at various chain lengths $N_p$, and various interaction strengths between solvent molecules and a polymer chain element. For self-diffusion coefficients D, the Einstein relation holds good; as chain length $N_p$ increases the D value decreases, and D also decreases as ${\varepsilon}_{cs}$ (the interaction parameter between the chain element and solvent molecules) increases. The relaxation time of velocity autocorrelation decreases as ${\varepsilon}_{cs}$ increases, and it is constant for various chain lengths. The diffusion coefficients in various conditions reveal that our systems are in a free draining limit as is well known from the behavior of low molecular weight polymers, this also agrees with the Kirkwood-Riesman theory.

• Bulletin of the Korean Chemical Society
• /
• v.13 no.3
• /
• pp.317-324
• /
• 1992

Structure and dynamics of $Na^+$ ions are investigated by molecular dynamics simulations of rigid dehydrated zeolite-A at several temperatures using a simple Lennard-Jones potential plus Coulomb potential. A best-fitted set of electrostatic charges is chosen from the results of simulation at 298.15 K and Ewald summation technique is used for the long-ranged character of Coulomb interaction. The calculated x, y, and z coordinates of $Na^+$ ions are in good agreement with the positions determined by X-ray crystallography within statistical errors, their random movings in different types of closed cages are well described by time-correlation functions, and $Na_Ⅰ$ type ions are found to be less diffusive than $Na_Ⅱ$ and $Na_{III}$. At 600.0 K, the unstable $Na_{III}$ type ion pushes down one of nearest $Na_{I}$ ions into the $\beta-cage$ and sits on the stable site Ⅰ, and the captured ion in the $\beta-cage$ wanders over and attacks one of 8 $Na_{I}$ type ions.

• Tribology and Lubricants
• /
• v.19 no.4
• /
• pp.230-236
• /
• 2003

In applications such as MEMS and NEMS devices, the adhesion force and contact load may be of the same order of magnitude and the static friction coefficient can be very large. Such large coefficient may result in unacceptable and possibly catastrophic adhesion, stiction, friction and wear. To obtain the static friction coefficient of contacting real surfaces without the assumption of an empirical coefficient value, numerical simulations of the contact load, tangential force, and adhesion force are preformed. The surfaces in dry contact are statistically modeled by a collection of spherical asperities with Gaussian height distribution. The asperity micro-contact model utilized in calculation (the ZMC model), considers the transition from elastic deformation to fully plastic flow of the contacting asperity. The force approach of the modified DMT model using the Lennard-Jones attractive potential is applied to characterize the intermolecular forces. The effect of the surface topography on the static friction coefficient is investigated for cases rough, intermediate, smooth, and very smooth, respectively. Results of the static friction coefficient versus the external force are presented for a wide range of plasticity index and surface energy, respectively. Compared with those obtained by the GW and CEB models, the ZMC model is more complete in calculating the static friction coefficient of rough surfaces.

• Structural Engineering and Mechanics
• /
• v.30 no.2
• /
• pp.177-190
• /
• 2008

Material failure behavior is generally dependent on loading rate. Especially in brittle and quasi-brittle materials, rate dependent material behavior can be significant. Empirical formulations are often used to predict the rate dependency, but such methods depend on extensive experimental works and are limited by practical constraints of physical testing. Numerical simulation can be an effective means for extracting knowledge about rate dependent behavior and for complementing the results obtained by testing. In this paper, the failure behavior of a brittle material under different loading rates is simulated by molecular dynamics analysis. A notched specimen is modeled by sub-million particles with a normalization scheme. Lennard-Jones potential is used to describe the interparticle force. Numerical simulations are performed with six different loading rates in a direct tensile test, where the loading velocity is normalized to the ratio of the pseudo-sonic speed. As a consequence, dynamic features are achieved from the numerical experiments. Remarkable failure characteristics, such as crack surface interaction/crack arrest, branching, and void nucleation, vary in case of the six loading cases. These characteristics are interpreted by the energy concept approach. This study provides insight into the change in dynamic failure mechanism under different loading rates.