• Proceedings of the Korean Society of Precision Engineering Conference
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• 2010.05a
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• pp.569-570
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• 2010

• Journal of Korean Vacuum Science & Technology
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• v.6 no.1
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• pp.22-29
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• 2002

The process of energetic deposition has been simulated by using molecular dynamics (W) simulation and kinetic Monte Carlo (KMC) simulation. The atomistic mechanisms of film growth in energetic deposition are discussed.

• Bulletin of the Korean Chemical Society
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• v.34 no.2
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• pp.574-578
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• 2013

In this work, the friction and diffusion coefficients of a tracer in a mesoscopic solvent are evaluated as a function of the tracer size by a hybrid molecular dynamics simulation where solute molecules evolve by Newton's equations of motion but the solvent evolves through the multi-particle collision dynamics. The friction coefficient is shown to scale linearly with the tracer size for larger tracers in accord with predictions of hydrodynamic theories. The diffusion coefficient of tracer is found to be inversely proportional to tracer size. The behavior of Stokes-Einstein formula is validated as a function of tracer size.

• 한국전산유체공학회:학술대회논문집
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• 2009.04a
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• pp.368-376
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• 2009

Studies on the effect of the wall-ion, wall-water, water-ion and ion-ion interaction on properties of water and ions in nano-channels have been performed through the use of different kinds of ions or different models of potential energy between wall-ion or wall-water. On this paper, we address the effect of water-wall interaction potential on the properties of confined aqueous solution by using the molecular dynamics (MD) simulations. As the interaction potential energies between water and wall we employed the models of the Weeks-Chandler-Andersen (WCA) and Lennard-Jones (LJ). On the MD simulations, 680 water molecules and 20 ions are included between uniformly charged plates that are separated by 2.6 nm. The water molecules are modeled by using the rigid SPC/E model (simple point charge/Extended) and the ions by the charged Lennard-Jones particle model. We compared the results obtained by using WCA potential with those by LJ potential. We also compared the results (e.g. ion density and electro-static potential distributions) in each of the above cases with those provided by solving the Poisson-Boltzmann equation.

• Proceedings of the Materials Research Society of Korea Conference
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• 2003.11a
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• pp.39-39
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• 2003

Molecular dynamics (MD) simulation was performed to study the stress induced grain boundary migration caused by the interaction of dislocations with a gain boundary. The simulation was carried out in a Ni block (295020 atoms) with a ∑ = 5 (210) grain boundary and an embedded atom potential for Ni was used for the MD calculation. Stress was provided by indenting a diamond indenter and the interaction between Ni surface and diamond indenter was assumed to have a fully repulsive force to emulate a faction free surface. Results showed that the indentation nucleated perfect dislocations and the dislocations produced stacking faults in the form of a parallelepiped tube. The parallelepiped tube consisted of two pairs of parallel dislocations with Shockley partials and was produced successively during the penetration of the indenter. The dislocations propagated along the parallelepiped slip planes and fully merged onto the ∑ = 5 (210) grain boundary without emitting a dislocation on the other grain. The interaction of the dislocations with the grain boundary induced the migration of the grain boundary plane in the direction normal to the boundary plane and the migration continued as long as the dislocations merged onto the grain boundary plane. The detailed mechanism of the conservative motion of atoms at the gram boundary was associated with the geometric feature of the ∑ = 5 (210) grain boundary.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.1
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• pp.24-29
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• 2014

Atomistic molecular dynamics (MD) simulation has become mature enabling close approximation of the real behaviors of biomolecules. In biomolecular NMR field, atomistic MD simulation coupled with generalized implicit solvent model (GBIS) has contributed to improving the qualities of NMR structures in the refinement stage with experimental restraints. Here all-atom force fields play important roles in defining the optimal positions between atoms and angles, resulting in more precise and accurate structures. Despite successful applications in refining NMR structure, however, the research that has studied the influence of force fields in GBIS is limited. In this study, we compared the qualities of NMR structures of two model proteins, ubiquitin and GB1, under a series of AMBER force fields-ff99SB, ff99SB-ILDN, ff99SB-NMR, ff12SB, and ff13-with experimental restraints. The root mean square deviations of backbone atoms and packing scores that reflect the apparent structural qualities were almost indistinguishable except ff13. Qualitative comparison of parameters, however, indicates that ff99SB-ILDN is more recommendable, at least in the cases of ubiquitin and GB1.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.2
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• pp.58-62
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• 2014

Human transmembrane proteins (hTMPs) are closely related to transport, channel formation, signaling, cell to cell interaction, so they are the crucial target of modern medicinal drugs. In order to study the structure and function of these hTMPs, it is important to prepare reasonable amounts of proteins. However, their preparation is seriously difficult and time-consuming due to insufficient yields and low solubility of hTMPs. We tried to produce large amounts of Syndecan-4 transmembrane domain (Syd4-TM) that is related to the healing wounds and tumor for a long time. In this study, we performed the structure determination of Syd4-TM combining the Polarity Index at Slanted Angle (PISA) wheel pattern analysis based on $^{15}N-^1H$ 2D SAMPI-4 solid-state NMR of expressed Syd4-TM and Molecular Dynamics (MD) simulation using Discovery Studio 3.1.

• Interaction and multiscale mechanics
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• v.4 no.3
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• pp.173-185
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• 2011

A multiscale modeling scheme that addresses the influence of the nanoparticle size in nanocomposites consisting of nano-sized spherical particles embedded in a polymer matrix is presented. A micromechanics-based constitutive model for nanoparticle-reinforced polymer composites is derived by incorporating the Eshelby tensor considering the interface effects (Duan et al. 2005a) into the ensemble-volume average method (Ju and Chen 1994). A numerical investigation is carried out to validate the proposed micromechanics-based constitutive model, and a parametric study on the interface moduli is conducted to investigate the effect of interface moduli on the overall behavior of the composites. In addition, molecular dynamics (MD) simulations are performed to determine the mechanical properties of the nanoparticles and polymer. Finally, the overall elastic moduli of the nanoparticle-reinforced polymer composites are estimated using the proposed multiscale approach combining the ensemble-volume average method and the MD simulation. The predictive capability of the proposed multiscale approach has been demonstrated through the multiscale numerical simulations.

• Nuclear Engineering and Technology
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• v.52 no.7
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• pp.1537-1544
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• 2020

Molecular dynamics (MD) simulations were conducted to investigate the temperature effects on the primary damage in gallium nitride (GaN) material. Five temperatures ranging from 300 K to 900 K were studied for 10 keV Ga primary knock-on atom (PKA) with inject direction of [0001]. The results of MD simulations showed that threshold displacement energy (E_d) was affected by temperatures and at higher temperature, it was larger. The evolutions of defects under various temperatures were similar. However, the higher temperature was found to increase the peak number, peak time, final time and recombination efficiency while decreasing the final number. With regard to clusters, isolated point defects and little clusters were common clusters and the fraction of point defects increased with temperature for vacancy clusters, whereas it did not appear in the interstitial clusters. Finally, at each temperature, the number of Ga interstitial atoms was larger than that of N and besides that, there were other different results of specific types of split interstitial atoms.

• Bulletin of the Korean Chemical Society
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• v.19 no.4
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• pp.422-428
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• 1998

In the present paper, we report a molecular dynamics (MD) simulation of non-rigid zeolite-A framework only as the base case for a consistent study of the role of intraframework interaction on several zeolite-A systems using the same technique in our previous studies of rigid zeolite-A frameworks. Usual bond stretching, bond angle bending, torsional rotational, and non-bonded Lennard-Jones and electrostatic interactions are considered as intraframework interaction potentials. The comparison of experimental and calculated structural parameters confirms the validity of our MD simulation for zeolite-A framework. The radial distribution functions of non-rigid zeolite-A framework atoms characterize the vibrational motion of the framework atoms. Mean square displacements are all periodic with a short period of 0.08 ps and a slow change in the amplitude of the vibration with a long period of 0.53 ps. The displacement auto-correlation (DAC) and neighbor-correlation (DNC) functions describe the up-and-down motion of the framework atoms from the center of α-cage and the back-and-forth motion on each ring window from the center of each window. The DAC and DNC functions of the framework atoms from the center of α-cage at the 8-ring windows have the same period of the up-and-down motion, but those functions from the center of 8-ring window at the 8-ring windows are of different periods of the back-and-forth motion.