• Journal of Biomedical Engineering Research
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• v.24 no.5
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• pp.447-451
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• 2003

A new method for analyzing the bone-remodeling process using quasi-molecular dynamics was proposed in this study. The effect of pressure due to bone marrow, which could not be considered in previous methods, was also considered in this method. Bone-remodeling response of the 2D vertebral body of lumbar spine to a uniaxial compressive displacement of 1.8564mm. corresponding to approximately 2kN of compressive load, was studied. Converged shape change of the cortical shell and rearrangement of cancellous bone structure matched well with a normal shape of the vertebral body. The calculated responses in the spinal elements also shows closed results compared with experimental results.

• 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.

• Interaction and multiscale mechanics
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• v.1 no.2
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• pp.303-315
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• 2008

In this paper, thermodynamical properties of crystalline silicon under strain are calculated using classical molecular dynamics (MD) simulations based on the Tersoff interatomic potential. The Helmholtz free energy of the silicon crystal under strain is calculated by using the ensemble method developed by Frenkel and Ladd (1984). To account for quantum corrections under strain in the classical MD simulations, we propose an approach where the quantum corrections to the internal energy and the Helmholtz free energy are obtained by using the corresponding energy deviation between the classical and quantum harmonic oscillators. We calculate the variation of thermodynamic properties with temperature and strain and compare them with results obtained by using the quasi-harmonic model in the reciprocal space.

• Journal of the Korean Vacuum Society
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• v.12 no.4
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• pp.281-287
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• 2003

We have performed classical molecular dynamics simulations for hypothetical silicon nanotubes using the Tersoff potential. Our investigation presented a systematic study about the thermal behavior of hypothetical silicon nanotubes and showed the difficulty in Producing silicon nanotubes or graphitelike sheets. Through the investigations on the structure and properties of a double-wall silicon nanotube, we concluded that quasi-one dimensional structures consisting of silicon atoms become nanowires or multi wall nanotubes rather than single wall nanotubes in order to minimize the number of $sp^2$ bonds.

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

• Proceedings of the Korean Vacuum Society Conference
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• 2009.02a
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• pp.100.2-100.2
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• 2009

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.21-21
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• 2011

A series of Quasi-Elastic Neutron Scattering (QENS) experiments helps us to understand the single-particle (hydrogen atom) dynamics of a globular protein and its hydration water and strong coupling between them. We also performed Molecular Dynamics (MD) simulations on a realistic model of the hydrated hen-egg Lysozyme powder having two proteins in the periodic box. We found the existence of a Fragile-to-Strong dynamic Crossover (FSC) phenomenon in hydration water around a protein occurring at TL=$225{\pm}5K$ by analyzing Intermediate Scattering Function (ISF). On lowering of the temperature toward FSC, the structure of hydration water makes a transition from predominantly the High Density Liquid (HDL) form, a more fluid state, to predominantly the Low Density Liquid (LDL) form, a less fluid state, derived from the existence of a liquid?liquid critical point at an elevated pressure. We showed experimentally and confirmed theoretically that this sudden switch in the mobility of the hydration water around a protein triggers the dynamic transition (so-called glass transition) of the protein, at a temperature TD=220 K. Mean Square Displacement (MSD) is the important factor to show that the FSC is the key to the strong coupling between a protein and its hydration water by suggesting TL${\fallingdotseq}$TD. MD simulations with TIP4P force field for water were performed to understand hydration level dependency of the FSC temperature. We added water molecules to increase hydration level of the protein hydration water, from 0.30, 0.45, 0.60 and 1.00 (1.00 is the bulk water). These confirm the existence of the FSC and the hydration level dependence of the FSC temperature: FSC temperature is decreased upon increasing hydration level. We compared the hydration water around Lysozyme, B-DNA and RNA. Similarity among those suggests that the FSC and this coupling be universal for globular proteins, biopolymers.

• Journal of the Korean Vacuum Society
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• v.7 no.s1
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• pp.183-189
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• 1998

A new computer simulation method for film growth, the kinetic Monte Carlo simulation in combination with the results obtained from molecular dynamics simulation for the transient process induced by deposited atoms, was developed. The behavior of energetic atom in Au/Au(100) thin film deposition was investigated by the method. The atomistic mechanism of energetic atom deposition that led to the smoothness enhancement and the relationship between the role of transient process and film growth mechanism were discussed. We found that energetic atoms cannot affect the film growth mode in layer-by-layer at high temperature. However, at temperature of film growth in 3-dimensional mode and in quasi-two-dimensional mode, energetic atoms can enhance the smoothness of film surface. The enhancement of smoothness is caused by the transient mobility of energetic atoms and the suppression for the formation of 3-dimensional islands.

• Korea-Australia Rheology Journal
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• v.13 no.1
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• pp.1-12
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• 2001

This paper describes the application of our recently developed two-phase model for flow-induced crystallization (FIC) to the simulation of fiber spinning and film blowing. 1-D and 2-D simulations of fiber spinning include the combined effects of (FIC), viscoelasticity, filament cooling, air drag, inertia, surface tension and gravity and the process dynamics are modeled from the spinneret to the take-up roll device (below the freeze point). 1-D model fits and predictions are in very good quantitative agreement with high- and low-speed spinline data for both nylon and PET systems. Necking and the associated extensional softening are also predicted. Consistent with experimental observations, the 2-D model also predicts a skin-core structure at low and intermediate spin speeds, with the stress, chain extension and crystallinity being highest at the surface. Film blowing is simulated using a "quasi-cylindrical" approximation for the momentum equations, and simulations include the combined effects of flow-induced crystallization, viscoelasticity, and bubble cooling. The effects of inflation pressure, melt extrusion temperature and take-up ratio on the bubble shape are predicted to be in agreement with experimental observations, and the location of the frost line is predicted naturally as a consequence of flow-induced crystallization. An important feature of our FIC model is the ability to predict stresses at the freeze point in fiber spinning and the frost line in film blowing, both of which are related to the physical and mechanical properties of the final product.l product.