• 한국전기전자재료학회논문지
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• 제16권12S호
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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.

• EDISON SW 활용 경진대회 논문집
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• 제2회(2013년)
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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.

• Bulletin of the Korean Chemical Society
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• 제20권5호
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• pp.587-591
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• 1999

A molecular dynamics simulation study on the structure and dynamics of Na+ ions in non-rigid dehydrated Na12-A zeolite framework at 298.15 K was conducted using the same method reported in previous studies on rigid and non-rigid Na12-A zeolite frameworks. The agreement between the experimental and calculated results for the zeolite-A framework atoms of structural parameters for non-rigid dehydrated Na12-A zeolite is generally quite good, and for the adsorbed Na+ions the agreement is acceptable. The calculated bond lengths are generally in good agreement with the experimental results and other theoretical data. The calculated IR spectrum by Fourier transform of the total dipole moment autocorrelation function shows two major peaks around 2700 cm-1 and 7000 cm-1. The former appeared in the calculated IR spectra of non-rigid zeolite-A framework only system and the latter remains unexplained except, perhaps, indicating a new formation of a vibrational mode of the framework due to the adsorption of Na+ ions. The peaks above 6200-6800 cm-1 in non-rigid dehydrated Nal2-A zeolite are much larger than those in non-rigid dehydrated H12-A zeolite.

• 멤브레인
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• 제26권5호
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• pp.329-336
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• 2016

수소이온 교환막(PEM; Proton Exchange Membrane)은 연료전지 막-전극 복합체(MEA; Membrane-electrode Assembly)를 구성하는 핵심 소재 중 하나로서, 촉매와 함께 연료전지 성능을 결정하는 중요한 역할을 한다. 이러한 수소이온교환막의 성능은 내부에 존재하는 수소이온 전달 통로인 수화 채널의 구조에 큰 영향을 받는 것으로 알려져 있다. 분자 동역학(MD; Molecular Dynamics) 전산모사 기술은 이러한 소재 내부의 분자 및 원자구조를 파악하기 위한 유용한 도구로서, 수소이온 교환막의 구조 및 특성에 관한 많은 관련 연구가 진행되고 있다. 본 총설에서는 분자동역학 전산모사 관련 연구에 대한 동향을 정리하고, 이를 통해 어떤 구조적 특징들을 분석할 수 있는지 제시하여, 수소이온 교환막 연구자들과 분리막 연구자들에게 분자동역학 전산모사 기술의 유용성에 대하여 소개하고자 한다.

• 멤브레인
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• 제30권6호
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• pp.433-442
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• 2020

본 연구에서는 수전해용 ionomer의 분자동역학 전산모사 모델 제작을 위하여, 과량의 물 분자가 존재하는 수전해 시스템의 특성을 반영한 ionomer 모델을 제작한 후, 기존 연료전지용 전해질막 전산모사 조건에 맞춰 제작한 ionomer 모델과 비교하였다. 최종적으로 얻어진 모델은 과불소계 ionomer의 중요 특징 중 하나인 명확한 상분리 및 수화채널이 관찰되었으며, 과량의 물 및 높은 운전 온도 조건에서도 물에 녹지 않고 안정된 구조를 나타내었다. 제조된 ionomer 모델에서는 과량의 물분자로 인한 이온 희석 효과로 이온 전달 성능 감소가 나타났으며, 반대로 수소 기체의 투과는 더 증가할 것으로 분석되었다. 따라서 이러한 수전해 시스템의 특성을 반영한 수전해용 ionomer 분자 구조 설계 전략이 필요하고, 분자동역학 전산모사 연구 시에도 이를 감안한 수전해용 ionomer 모델 제작이 필요하다.

• Macromolecular Research
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• 제12권2호
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• pp.178-188
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• 2004

We performed molecular dynamics (MD) simulations at 300 K on a series of poly(benzyl ether) (PBE) dendrimers having a different core functionalities. We used the rotational isomeric state Metropolis Monte Carlo (RMMC) method to construct the initial configuration in a periodic boundary cell (PBC) before the MD simulations were undertaken. To elucidate the effects that the structural features have on the chain dimension, the overall internal structure, and the morphology, we monitored the radii of gyration, R$\sub$g/ and the conformational changes during the simulations. The PBE dendrimers in a glassy state adopted less-extended structures when compared with the conformations obtained from the RMMC calculations. We found that R$\sub$g/ of the PBE dendrimer depends on the molecular weight, M, according to the relation, R$\sub$g/∼M$\^$0.22/. The radial distributions of the dendrimers were developed identically in the PBC, irrespective of the core functionality. A gradual decrease in radial density resulted from the fact that the terminal branch ends are distributed all over the molecule, except for the core region.

• Bulletin of the Korean Chemical Society
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• 제35권7호
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• pp.2097-2108
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• 2014

Chemical feature based quantitative pharmacophore models were generated using the HypoGen module implemented in DS2.5. The best hypothesis, Hypo1, which was characterized by the highest correlation coefficient (0.96), the highest cost difference (61.60) and the lowest RMSD (0.74), consisted of one hydrogen bond acceptor, one hydrogen bond donor, one hydrophobic and one ring aromatic. The reliability of Hypo1 was validated on the basis of cost analysis, test set, Fischer's randomization method and GH test method. The validated Hypo1 was used as a 3D search query to identify novel inhibitors. The screened molecules were further refined by employing ADMET, docking studies and visual inspection. Three compounds with novel scaffolds were selected as the most promising candidates for the designing of Mcl-1 antagonists. Finally, a 10 ns molecular dynamics simulation was carried out on the complex of receptor and the retrieved ligand to demonstrate that the binding mode was stable during the MD simulation.

• Bulletin of the Korean Chemical Society
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• 제30권11호
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• pp.2723-2728
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• 2009

The conformational properties of oligosaccharides are important to understand carbohydrate-protein interactions. A trimannoside, methyl 3,6-di-O-($\alpha$-D-Man)-$\alpha$-D-Man (TRIMAN) is a basic unit of N-linked oligosaccharides. This TRIMAN moiety was further modified by GlcNAc (BISECT), which is important to biological activity of N-glycan. To characterize the trimannoside and its bisecting one we performed a molecular dynamics simulation in water. The resulting models show the conformational transition with two major and minor conformations. The major conformational transition results from the $\omega$ angle transition; another minor transition is due to the $\psi$ angle transition of $\alpha$ (1 $\rightarrow$ 6) linkage. The introduction of bisecting GlcNAc on TRIMAN made the different population of the major and minor conformations of the TRIMAN moiety. Omega ($\omega$) angle distribution is largely changed and the population of gt conformation is increased in BISECT oligosaccharide. The inter-residue hydrogen bonds and water bridges via bisecting GlcNAc residue make alterations on the local and overall conformation of TRIMAN moiety. These changes of conformational distribution for TRIMAN moiety can affect the overall conformation of N-glycan and the biological activity of glycoprotein.

• Bulletin of the Korean Chemical Society
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• 제17권8호
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• pp.700-706
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• 1996

We present the results of molecular dynamics simulations of monolayers of long-chain alkyl thiol [S(CH2)15CH3] molecules on an air-solid interface using the extended collapsed atom model for the chain-molecule and a gold surface for the solid surface. Several molecular dynamics simulations have been performed on monolayers with areas per molecule ranging from 18.30 to 32.10 Å2/molecule. It is found that there exist three possible transitions: a continuous transition characterized by a change in molecular configuration without change in lattice structure, a sudden transition characterized by the distinct lattice defects and perfect islands, and a third transition characterized by the appearance of a random, liquid-like state. The analysis of probability distributions of the segments shows that the structure of the chain-molecules at the air-solid interface is completely different from that at the air-water interface in the view of the degree of overlap of the probability distributions of the neighbor segments. The calculated diffusion coefficients of the chain-molecules on the monolayers seem to be not directly related to any one of the three transitions. However, the large diffusion of the molecules enhanced by the increment of the area per molecule may induce the second transition.

• Macromolecular Research
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• 제9권3호
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• pp.129-142
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• 2001

To efficiently demonstrate the molecular motion, physical properties, and mechanical properties of polycarbonates, we studied the differences between bisphenol-A polycarbonate(BPA-PC) and tetramethyl bisphenol-A-polycarbonate(TMBPA-PC) using molecular modeling techniques. To investigate the conformations of BPA-PC and TMBPA-PC and the effect of the conformation on mechanical properties, we performed conformational energy calculation, molecular dynamics calculation, and stress-strain curves based on molecular mechanics method. From the result obtained from conformational energy calculations of each segment, the molecular motions of the carbonate and the phenylene group in BPA-PC were seen to be more vigorous and have lower restriction to mobility than those in TMBPA-PC, respectively. In addition, from the results of radial distribution function, velocity autocorrelation function, and power spectrum, BPA-PC appeared to have higher diffusion constant than TMBPA-PC and is easier to have various conformations because of the less severe restrictions in molecular motion. The result of stress-strain calculation for TMBPA-PC seemed to be in accordance with the experimental value of strain-to-failure ∼4%. From these results of conformational energy calculations of segments, molecular dynamics, and mechanical properties, it can be concluded that TMBPA-PC has higher modulus and brittleness than BPA-PC because the former has no efficient relaxation mode against the external deformations.