• Proceedings of the KSME Conference
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• 2007.05b
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• pp.1912-1915
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• 2007

The disjoining pressure is critical in modeling the transport phenomena in small scales. They are very useful in characterizing the non-continuum effects that are not negligible in heat and mass transports in the film of less than submicro-scales. We present he disjoining pressure of thin film absorbed on solid substrate using Molecular Dynamics Simulation (MD). The disjoining pressure with respect to the film thickness is accurately calculated in the resolution of a molecular scale. The characteristics of the pressure are discussed regarding the molecular nature of the fluid system like molecular diameter and intermolecular interaction. Also, the MD results are compared with those based on the macroscopic approximation of the slab-like density profile. Significant discrepancy is observed when the effective film thickness is less than several molecular diameter

• Journal of the Korean Chemical Society
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• v.56 no.6
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• pp.669-672
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• 2012

Classical molecular dynamics (MD) simulations using a scaled OSS2 potential originally derived from ab initio calculations are used to study the radial distribution functions of water. The original OSS2 water potential is shown to represent a glassy or an ice at ambient temperature, but the diffusion coefficient increases on increasing the temperature of the system or decreasing the density. This suggests scaling the OSS2 potential. The O-O, O-H, and H-H radial distribution functions and the corresponding coordination numbers for the scaled OSS2 potential, obtained by MD simulation, are in good agreement with the experiment results and calculations for the SPC/E water potential over a range of temperatures.

• Bulletin of the Korean Chemical Society
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• v.32 no.11
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• pp.3909-3913
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• 2011

In this paper we have carried out molecular dynamics simulations (MD) for model systems of liquid n-alkane oligomers ($C_{12}{\sim}C_{80}$) at high temperatures (~2300 K) in a canonical ensemble to calculate viscosity ${\eta}$, self-diffusion constants D, and monomeric friction constant ${\zeta}$. We found that the long chains of these n-alkanes at high temperatures show an abnormality in density and in monomeric friction constant. The behavior of both activation energies, $E_{\eta}$ and $E_D$, and the mass and temperature dependence of ${\eta}$, D, and ${\zeta}$ are discussed.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.506-511
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• 2007

Mechanical behavior of copper nanowire is investigated. An FCC nanowire model composed of 1,408 atoms is used for MD simulation. Simulations are performed within NVT ensemble setting without periodic boundary conditions. $Nos\acute{e}-Poincar\acute{e}$ MD algorithm is employed to guarantee preservation of Hamiltonian and temperature. Numerical tensile tests of Nanowire are carried out with constant strain rate. Additionally, temperature and strain rate effects are considered. Stress-strain curve is constructed from the calculated Cauchy stresses and specified strain values. In (22,4,4) Copper nanowire, non-linear behavior appears around ${\epsilon}\simeq0.09.$ At this instance, starting of structural reorientations are observed. At the onset of reorientation, the modulus characteristics are also investigated.

• Interaction and multiscale mechanics
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• v.4 no.3
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• pp.219-237
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• 2011

Recent advances in scientific computing enable the full atomistic simulation of DNA molecules. However, there exists length and time scale limitations in molecular dynamics (MD) simulation for large DNA molecules. In this work, a two-level homogenization of DNA molecules is proposed. A wavelet projection method is first introduced to form a coarse-grained DNA molecule represented with superatoms. The coarsened MD model offers a simplified molecular structure for the continuum description of DNA molecules. The coarsened DNA molecular structure is then homogenized into a three-dimensional beam with embedded molecular properties. The methods to determine the elasticity constants in the continuum model are also presented. The proposed continuum model is adopted for the study of mechanical behavior of DNA loop.

• Proceedings of the IEEK Conference
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• 2003.07b
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• pp.735-738
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• 2003

In this paper, we report a molecular dynamics (MD) simulation of the ion implantation for nano-scale devices with ultra-shallow junctions. In order to model the profile of ion distribution in nanometer scale, the molecular dynamics with a damage model has been employed. As an exemplary case, we calculate the dopant profile during the ion implantation of B, As, and Ge.

• Journal of the Korean Society of Manufacturing Process Engineers
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• v.8 no.1
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• pp.43-47
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• 2009

Recently, an approach for nano-scale material deformation has been developed that couples the atomistic and continuum approaches using Finite Element Method (FEM) and Molecular Dynamics (MD). However, this approach still has problems to connect two approaches because of the difference of basic assumptions, continuum and atomistic modeling. To solve this problem, an alternative way is developed that connects the QuasiMolecular Dynamics (QMD) and molecular dynamics. In this paper, we suggest the way to make and validate the MD-QMD coupled model.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.32 no.12
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• pp.1047-1054
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• 2008

In this paper, the molecular dynamics (MD) simulations are performed with single-crystal copper blocks under simple shear and simple tension to investigate the effect of size and crystal orientation. There are many variances to give influences such as deformation path, temperature, specimen size and crystal orientation. Among them, the crystal orientation has a primary influence on the volume averaged stress. The numerical results show that the volume averaged shear stress decreases as the specimen size increases and as the crystal orientation changes from single to octal. Furthermore, the Schmid factor and yield stress for crystal orientation are evaluated by using the MD simulation on the standard triangle of stereographic projection.

• Bulletin of the Korean Chemical Society
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• v.23 no.3
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• pp.441-446
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• 2002

We have presented the results of thermodynamic, structural and dynamic properties of liquid benzene, toluene, and p-xylene in canonical (NVT) ensemble at 293.15 K by molecular dynamics (MD) simulations. The molecular model adopted for these molecules is a combination of the rigid body treatment for the benzene ring and an atomistically detailed model for the methyl hydrogen atoms. The calculated pressures are too low in the NVT ensemble MD simulations. The various thermodynamic properties reflect that the intermolecular interactions become stronger as the number of methyl group attached into the benzene ring increases. The pronounced nearest neighbor peak in the center of mass g(r) of liquid benzene at 293.15 K, provides the interpretation that nearest neighbors tend to be perpendicular. Two self-diffusion coefficients of liquid benzene at 293.15 K calculated from MSD and VAC function are in excellent agreement with the experimental measures. The self-diffusion coefficients of liquid toluene also agree well with the experimental ones for toluene in benzene and for toluene in cyclohexane.

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