• Tribology and Lubricants
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• 제21권4호
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• pp.177-184
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• 2005

The molecular dynamics simulation of nanoimprint lithography (NIL) using $SiO_2$ stamp and amorphous poly-(methylmethacrylate) (PNMA) film is performed to study pattern transfer in NIL. Force fields including bond, angle, torsion, van der Waals and electrostatic potential are used to describe the intermolecular and intramolecular force of PMMA molecules and $SiO_2$ stamp. Nose-Hoover thermostat is used to control the system temperature and cell multipole method is adopted to treat long range interactions. The deformation of PMMA film is observed during pattern transfer in the NIL process. For the detail analysis of deformation characteristics, the distributions of density and stress in PMHA film are calculated. The adhesion and friction forces are obtained by dividing the PMMA film into subregions and calculating the interacting force between subregion and stamp. Their effects on the pattern transfer are also discussed as varying the indentation depth and speed.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제40회 동계학술대회 초록집
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• pp.325-325
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• 2011

Very initial stage of oxidation process of Si (001) surface at room temperature (300 K) and high temperature (1200 K) was investigated using large scale molecular dynamics simulation. Reactive force field potential [1] was used for the simulation owing to its ability to handle charge variation as well as breaking and forming of bonds associated with the oxidation reaction. The results show that oxygen molecules adsorb dissociatively or otherwise leave the silicon surface. Initial position and orientation of oxygen molecule above the surface play important role in determining final state and time needed to dissociate. At 300 K, continuous transformation of ion $Si^+$ (or suboxide Si2O) to $Si2^+$ (SiO), $Si3^+$ (Si2O3) and finally to $Si4^+$ (SiO2) clearly observed. High temperature silicon surface provide heat energy that enable oxygen atom to penetrate into deeper silicon surface. The heat energy also retards adsorption process. As a result, transformation of ion $Si^+$ is impeded at 1200 K.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제40회 동계학술대회 초록집
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• pp.433-433
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• 2011

Since the concept of graphene was established, it has been intensively investigated by researchers. The unique characteristics of graphene have been reported, the graphene attracted a lot of attention for material overcomes the limitations of existing semiconductor materials. Because of these trends, economical fabrication technique is becoming more and more important topic. Especially, the epitaxial growth method by sublimating the silicon atoms on Silicon carbide (SiC) substrate have been reported on the mass production of high quality graphene sheets. Although SiC exists in a variety of polytypes, the 3C-SiC polytypes is the only polytype that grows directly on Si substrate. To practical use of graphene for electronic devices, the technique, forming the graphene on 3C-SiC(111)/Si structure, is much helpful technique. In this paper, we report on the growth of graphene on 3C-SiC(111) surface. To investigate the morphology of formed graphene on the 3C-SiC(111) surface, the radial distribution function (RDF) was calculated using molecular dynamics (MD) simulation. Through the comparison between the kinetic energies and the diffusion energy barrier of surface carbon atoms, we successfully determined that the graphitization strongly depends on temperature. This graphitization occurs above the annealing temperature of 1500K, and is also closely related to the behavior of carbon atoms on SiC surface. By analyzing the results, we found that the diffusion energy barrier is the key parameter of graphene growth on SiC surface.

• Bulletin of the Korean Chemical Society
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• 제29권2호
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• pp.408-412
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• 2008

FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1) in Arabidopsis are homologous proteins that perform opposite functions: FT is an activator of flowering, and TFL1 is a repressor. It was shown before that change of a single amino acid (His88) of TFL1 to the corresponding amino acid (Tyr) of FT is enough to convert the floral repressor to an activator. However, structural basis of the functional conversion has not been understood. In our molecular dynamics simulations on modified TFL1 proteins, a hydrogen bond present in native TFL1 between the His88 residue and a residue (Asp144) in a neighboring external loop became broken by change of His88 to Tyr. This breakage induced conformational change of the external loop whose structure was previously reported to be another key functional determinant. These findings reveal that the two important factors determining the functional specificities of the floral regulators, the key amino acid (His88) and the external loop, are correlated, and the key amino acid determines the functional specificity indirectly by affecting the conformation of the external loop.

• Bulletin of the Korean Chemical Society
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• 제29권2호
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• pp.363-371
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• 2008

As a computational method for the discovery of the effective agonists for PPARd, we address the usefulness of molecular dynamics free energy (MDFE) simulation with explicit solvent in terms of the accuracy and the computing cost. For this purpose, we establish an efficient computational protocol of thermodynamic integration (TI) that is superior to free energy perturbation (FEP) method in parallel computing environment. Using this protocol, the relative binding affinities of GW501516 and its derivatives for PPARd are calculated. The accuracy of our protocol was evaluated in two steps. First, we devise a thermodynamic cycle to calculate the absolute and relative hydration free energies of test molecules. This allows a self-consistent check for the accuracy of the calculation protocol. Second, the calculated relative binding affinities of the selected ligands are compared with experimental IC50 values. The average deviation of the calculated binding free energies from the experimental results amounts at the most to 1 kcal/mol. The computational efficiency of current protocol is also assessed by comparing its execution times with those of the sequential version of the TI protocol. The results show that the calculation can be accelerated by 4 times when compared to the sequential run. Based on the calculations with the parallel computational protocol, a new potential agonist of GW501516 derivative is proposed.

• Bulletin of the Korean Chemical Society
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• 제34권10호
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• pp.2925-2930
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• 2013

We present results of molecular dynamics simulations for hydroxide ion in supercritical water of densities 0.22, 0.31, 0.40, 0.48, 0.61, and 0.74 g/cc using the SPC/E water potential with Ewald summation. The limiting molar conductance of $OH^-$ ion at 673 K monotonically increases with decreasing water density. It is also found that the hydration number of water molecules in the first hydration shells around the $OH^-$ ion decreases and the potential energy per hydrated water molecule also decreases in the whole water density region with decreasing water density. Unlike the case in our previous works on LiCl, NaCl, NaBr, and CsBr [Lee at al., Chem. Phys. Lett. 1998, 293, 289-294 and J. Chem. Phys. 2000, 112, 864-869], the number of hydrated water molecules around ions and the potential energy per hydrated water molecule give the same effect to cause a monotonically increasing of the diffusion coefficient with decreasing water density in the whole water density region. The decreasing residence times are consistent with the decreasing potential energy per hydrated water molecule.

• Bulletin of the Korean Chemical Society
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• 제31권10호
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• pp.2903-2908
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• 2010

Protein S-nitrosation is common in cells under nitrosative stress. In order to model proteins with S-nitrosocysteine (CysSNO) residues, we first developed an Amber force field for S-nitrosoethanethiol (EtSNO) and then transferred it to CysSNO. Partial atomic charges for EtSNO and CysSNO were obtained by a restrained electrostatic potential approach to be compatible with the Amber-99 force field. The force field parameters for bonds and angles in EtSNO were obtained from a generalized Amber force field (GAFF) by running the Antechamber module of the Amber software package. The GAFF parameters for the CC-SN and CS-NO dihedrals were not accurate and thus determined anew. The CC-SN and CS-NO torsional energy profiles of EtSNO were calculated quantum mechanically at the level of B3LYP/cc-pVTZ//HF/6-$31G^*$. Torsional force constants were obtained by fitting the theoretical torsional energies with those obtained from molecular mechanics energy minimization. These parameters for EtSNO reproduced, to a reasonable accuracy, the corresponding torsional energy profiles of the capped tripeptide ACE-CysSNO-NME as well as their structures obtained from quantum mechanical geometry optimization. A molecular dynamics simulation of myoglobin with a CysSNO residue produced a well-behaved trajectory demonstrating that the parameters may be used in modeling other S-nitrosated proteins.

• 한국전기전자재료학회논문지
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• 제18권5호
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• pp.414-422
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• 2005

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. We proposed and investigated three mechanical models: (1) Constant Force Model; (2) Constant Depth Model, (3) Variable Force Model, and three chemical models, such as (1) Chemically Reactive Surface Model, (2) Chemically Passivating Surface Model, and (3) Chemically Passivating-reactive Surface Model. From the results obtained from classical molecular dynamics simulations for these models, we concluded that atomistic chemical mechanical polishing model based on both Variable Force Model and Chemically Passivating-reactive Surface Model were the most suitable for realistic simulation of chemical mechanical polishing in the atomic scale. The proposed model can be extended to investigate the 3-dimensional chemical mechanical polishing processes in the atomic scale.

• 대한금속재료학회지
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• 제47권1호
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• pp.32-37
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• 2009

Molecular dynamic simulations on the structural evolution of the Si(001) vicinal surfaces, which are tilted with respect to [100] and [110] directions were performed by using the empirical Tersoff potential. Tersoff potential was implemented at LAMMPS code and confirmed to describe the properties of Si. When the steps are generated along [100] direction, symmetric dimer rows formed with respect to the step edges. On the other hand, when the steps are generated along [110] direction, alternating dimer rows form with respect to the step edges. The configurational differences between the two vicinal surfaces were discussed in terms of the surface diffusion and the possibility of preventing step bunching for the (001) vicinal surface tilted along [100] direction was suggested.

• 한국전자통신학회논문지
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• 제14권1호
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• pp.147-154
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• 2019

이 연구에서는 분자들이 노즐과 터빈내부에서 운동하는 거동을 모사하기 위해 분자동력학 시뮬레이션 시스템의 모델을 설계하고 개발하였다. Lennard-Jones Potential 모델을 이용하여 분자들간에 상호 작용을 계산하고, Verlet 알고리듬을 뉴턴의 운동 방정식을 적산하기 위한 수치해석 방법으로 사용하였다. Lennard-Jones Potential 함수를 계산하기 위해, 분자 개수 N에 대해 $O(N^2)$ 계산량을 cutoff $r_c$를 이용하여 O(N)으로 줄여서 계산하여 CPU 시간을 절약할 수 있도록 구현하였다.