• 한국전산유체공학회:학술대회논문집
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• 2010.05a
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• pp.575-580
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• 2010

In this work, the electrophoretic motion of dsDNA molecule represented by a polymer through an artificial nano-pore in a membrane is simulated using the numerical method combining the lattice Boltzmann and Langevin molecular dynamic method. The polymer motion is represented by Langevin molecular dynamics technique while the fluid flow is taken into account by fluctuating lattice-Boltzmann method. The hydrodynamic interactions between the polymer and solvent in a confined space with a membrane having a hole are considered explicitly through the frictional and the random forces. The electric field intensity over the space is obtained from a finite difference method. Initially, the polymer is placed at one side of the space, and an electric field is applied to drive the polymer to the other side of the space through the nano-pore. In future, we plan to study the effect of the polymer size and the electric field on the electrophoretic velocity.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.300-300
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• 2011

Si oxidation is a key process in developing silicon devices, such as highly integrated metal-oxide-semiconductor (MOS) transistors and antireflection-coating (ARC) on solar cell substrate. Many experimental and theoritical studies have been carried out for elucidating oxidation processes and adsorption structure using ab initio total energy and electronic structure calcultaions. However, the initial oxidation processes at step edge on vicinal Si surface have not been studied using the ReaxFF reactive force field. In this work, strucutural change, charge distribution of oxidized Si throughout the depth from Si surface were observed during oxidation processes on vicinal Si(001) surface inclined by $10.5^{\circ}$ of miscut angle toward [100]. Adsorption energys of step edge and flat terrace were calculated to compare the oxidation reaction at step edge and flat terrace on Si surface.

• Transactions of the Korean hydrogen and new energy society
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• v.12 no.3
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• pp.191-199
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• 2001

In this paper molecular dynamics simulations have been carried out to investigate energy and momentum transfer of hydrogen ions impacted on the Ni (100) surface with $45^{\circ}$ and $90^{\circ}$ incident angles. The initial kinetic energies of the hydrogen ion were ranged from 100 eV to 1,600 eV to study the layer-by-layer energy variation as a dependence of incident energies and angles. At low incident energies, the scattering energy transfer is dominated by the normal motion of surface layers due to thermal vibrations and multiple collision effects. For higher incident energies, the scattering energy transfer in a normal direction is greater than that in a parallel direction. In the case of penetration, the amount of transferred energies do not affect much on Ni layers at low incident energy. It was found channeling effects through Ni layers with increasing incident energies.

• Transactions of the Korean hydrogen and new energy society
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• v.12 no.1
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• pp.51-63
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• 2001

In this paper molecular dynamics simulations were employed to investigate the structural and dynamic properties of hydrogen ions impacted on the Ni (100) surface with the $45^{\circ}$ incident angle. The initial kinetic energies of the hydrogen ion range from 100 to 1,600 eV. Together with the trajectory visualization of hydrogen ions, we computed scattering and penetration yields, mean energies and angles, and probability and energy distributions as a function of longitudinal and azimuthal directions. In the case of lower energy scattering ions, the multiple collision effects were found to be important to the third layers or lower. For higher energy penetrating ions, compared with the normal incident angle, it was significant the effective channeling effects through the Ni layers and the angle dependencies were indicated both in the longitudinal and the azimuthal angle directions.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.16 no.12S
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• pp.1157-1164
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• 2003

This paper shows the results of atomistic modeling for the interaction between spherical nano abrasive and substrate in chemical mechanical polishing processes. Atomistic modeling was achieved from 2-dimensional molecular dynamics simulations using the Lennard-Jones 12-6 potentials. The abrasive dynamics was modeled by three cases, such as slipping, rolling, and rotating. Simulation results showed that the different dynamics of the abrasive results the different features of surfaces. This model can be extended to investigate the 3-dimensional chemical mechanical polishing processes.

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1047-1050
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• 2013

Molecular dynamic simulations were performed to examine the wetting behavior of a graphite surface textured with nanoscale pillars. The contact angle of a water droplet on parallelepiped or dome-shaped pillars was investigated by systematically varying the height and width of the pillar and the spacing between pillars. An optimal inter-pillar spacing that gives the highest contact angle was found. The droplet on the dome-covered surface was determined to be more mobile than that on the surface covered with parallelepiped pillars.

• Transactions of the Korean Society of Mechanical Engineers B
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• v.29 no.1 s.232
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• pp.159-168
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• 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
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• v.30 no.5
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• pp.1139-1142
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• 2009

Refinement of NMR structures by molecular dynamics (MD) simulations with a solvent model has improved the structural quality. In this study, we applied MD refinement with the generalized Born (GB) implicit solvent model to protein structure determined under membrane-like environments. Despite popularity of the GB model, its applications to the refinement of NMR structures of hydrophobic proteins, in which detergents or organic solvents enclose proteins, are limited, and there is little information on the use of another GB parameter for these cases. We carried out MD refinement of crambin NMR structure in dodecylphosphocholine (DPC) micelles (Ahn et al., J. Am. Chem. Soc. 2006, 128, 4398-4404) with GB/Surface area model and two different surface tension coefficients, one for aquatic and the other for hydrophobic conditions. Our data show that, of two structures by MD refinement with GB model, the one refined with the parameter to consider hydrophobic condition had the better qualities in terms of precision and solvent accessibility.

• Proceeding of EDISON Challenge
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• 2013.04a
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• pp.1-12
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• 2013

그래핀에 대한 이론 연구는 주로 계산이 용이한 코스그레인 (Coarse-grained) 모델을 이용한 분자동역학 시뮬레이션을 토대로 이루어져 왔다. 하지만 그래핀 고분자 복합체, 표면이 개질된 그래핀의 구조 등에 대한 원자 수준의 총체적인 정보는 거시적인 (Macroscopic) 코스그레인 모델을 바탕으로 한 분자동역학 시뮬레이션으로는 얻을 수 없다. 따라서 본 연구에서는 전자구조 계산 및 원자 수준 모델의 Born Oppenheimer Molecular Dynamics를 이용하여 작은 그래핀 분자의 구조 (Structure)와 형태동역학 (Conformational Dynamics)에 대한 정보를 얻고, 이를 바탕으로 한 코스그레인 모델을 구축하였다. 더 나아가 이 코스그레인 모델을 이용하여 전기전도성 네트워크와 고분자-그래핀 복합체의 구조 등에 대해 살펴보고자 한다.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.7 no.2
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• pp.163-167
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• 2006

This paper shows a gigahertz actuator based on multi-wall carbon nanotubes(CNT) encapsulating metallic ions using classical molecular dynamics simulations. Encapsulated potassium ions accelerated by an applying external electric field could initialize a gigahertz actuator composed of a $7K^{+}(a)CNT$ oscillator.