• Bulletin of the Korean Chemical Society
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• 제33권3호
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• pp.862-868
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• 2012

Based on the recently derived general expression for the rates of diffusion-controlled reactions, we calculate the rates of dismutation of the superoxide anion radical catalyzed by Cu/Zn superoxide dismutases (SOD). This is the first attempt to calculate the absolute rates of diffusion-controlled enzyme reactions based on the atomiclevel molecular dynamics simulations. All solvent molecules are included explicitly and the effects of the structural flexibility of enzyme, especially those of side chain motions near the active site, are included in the present calculation. In addition, the actual mobility of the substrate molecule is taken into account, which may change as the molecule approaches the active site of enzyme from the bulk solution. The absolute value of the rate constant for the wild type SOD reaction obtained from MD simulation is shown to be in good agreement with the experimental value. The calculated reactivity of a mutant SOD is also in agreement with the experimental result.

• 한국환경과학회지
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• 제25권7호
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• pp.927-935
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• 2016

Dissolved oxygen is necessary for many biological processes as well as many industrial practices. Dissolved oxygen released from water in dissolved air flotation (DAF) systems can be have many different applications. However, DAF systems are very costly to operate. To develop more efficient DAF systems, a deeper understanding of the process of oxygen being released from water is required. In this study, molecular dynamics (MD) simulations were used to simulate 100 oxygen molecules surrounded by 31002 water molecules at temperatures ranging from $0^{\circ}C$ to $100^{\circ}C$. Simulations were carried out for 10 ns, during which, in most cases, all the oxygen molecules were released from the water droplet. With MD simulations, visualization of the molecules escaping the water droplet was possible, which aided the understanding of the interactions between molecules at the nano-scale. The results showed that as the oxygen molecules moved near the edge of the water droplet that the oxygen molecules hesitated before escaping the water droplet or returned to the interior of the water droplet. This was because of the attractive forces between the water and oxygen molecules. Moreover, after most of the oxygen molecules were released from the droplet, some were found to return to the droplet's edge or even the interior of the droplet. It was also confirmed that oxygen molecules were released at a faster rate at higher temperatures.

• Bulletin of the Korean Chemical Society
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• 제35권3호
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• pp.783-792
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• 2014

The binding interaction between a hemolytic peptide ${\delta}$-lysin and a zwitterionic lipid bilayer POPC was investigated through a series of molecular dynamics (MD) simulations. ${\delta}$-Lysin is a 26-residue, amphipathic, ${\alpha}$-helical peptide toxin secreted by Staphylococcus aureus. Unlike typical antimicrobial peptides, ${\delta}$-lysin has no net charge and it is often found in aggregated forms in solution even at low concentration. Our study showed that only the monomer, not dimer, inserts into the bilayer interior. The monomer is preferentially attracted toward the membrane with its hydrophilic side facing the bilayer surface. However, peptide insertion requires the opposite orientation where the hydrophobic side of peptide points toward the membrane interior. Such orientation allows the charged residues, Lys and Asp, to have stable salt bridges with the lipid head-group while the hydrophobic residues are buried deeper in the hydrophobic lipid interior. Our simulations suggest that breaking these salt bridges is the key step for the monomer to be fully inserted into the center of lipid bilayer and, possibly, to translocate across the membrane.

• 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.

• Nuclear Engineering and Technology
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• 제50권6호
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• pp.907-914
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• 2018

In this article, we conducted molecular dynamics simulations to investigate the effect of applied strain and temperature on irradiation-induced damage in alpha-zirconium. Cascade simulations were performed with primary knock-on atom energies ranging between 1 and 20 KeV, hydrostatic and uniaxial strain values ranging from -2% (compression) to 2% (tensile), and temperatures ranging from 100 to 1000 K. Results demonstrated that the number of defects increased when the displacement cascade proceeded under tensile uniaxial hydrostatic strain. In contrast, compressive strain states tended to decrease the defect production rate as compared with the reference no-strain condition. The proportions of vacancy and interstitial clustering increased by approximately 45% and 55% and 25% and 32% for 2% hydrostatic and uniaxial strain systems, respectively, as compared with the unstrained system, whereas both strain fields resulted in a 15-30% decrease in vacancy and interstitial clustering under compressive conditions. Tensile strains, specifically hydrostatic strain, tended to produce larger sized vacancy and interstitial clusters, whereas compressive strain systems did not significantly affect the size of defect clusters as compared with the reference no-strain condition. The influence of the strain system on radiation damage became more significant at lower temperatures because of less annealing than in higher temperature systems.

• 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.

• 한국정보디스플레이학회:학술대회논문집
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• 한국정보디스플레이학회 2008년도 International Meeting on Information Display
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• pp.1049-1052
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• 2008

We developed novel molecular dynamics and quantum chemical molecular dynamics simulators for the design of MgO protecting layer in plasma display panel. These simulators were applied to the investigations on the destruction processes of the MgO protecting layer as well as the evaluation of its second electron emission ability. From the simulation results, we successfully proposed new guidelines for MgO protecting layer with high durability and high second electron emission ability.

• Bulletin of the Korean Chemical Society
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• 제31권9호
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• pp.2581-2587
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• 2010

Nitration of tyrosine and tryptophan residues is common in cells under nitrative stress. However, physiological consequences of protein nitration are not well characterized on a molecular level due to limited availability of the 3D structures of nitrated proteins. Molecular dynamics (MD) simulation can be an alternative tool to probe the structural perturbations induced by nitration. In this study we developed molecular mechanics parameters for 3-nitrotyrosine (NIY) and 6-nitrotryptophan (NIW) that are compatible with the AMBER-99 force field. Partial atomic charges were derived by using a multi-conformational restrained electrostatic potential (RESP) methodology that included the geometry optimized structures of both $\alpha$- and $\beta$-conformers of a capped tripeptide ACE-NIY-NME or ACE-NIW-NME. Force constants for bonds and angles were adopted from the generalized AMBER force field. Torsional force constants for the proper dihedral C-C-N-O and improper dihedral C-O-N-O of the nitro group in NIY were determined by fitting the torsional energy profiles obtained from quantum mechanical (QM) geometry optimization with those from molecular mechanical (MM) energy minimization. Force field parameters obtained for NIY were transferable to NIW so that they reproduced the QM torsional energy profiles of ACE-NIW-NME accurately. Moreover, the QM optimized structures of the tripeptides containing NIY and NIW were almost identical to the corresponding structures obtained from MM energy minimization, attesting the validity of the current parameter set. Molecular dynamics simulations of thioredoxin nitrated at the single tyrosine and tryptophan yielded well-behaved trajectories suggesting that the parameters are suitable for molecular dynamics simulations of a nitrated protein.

• Biomolecules & Therapeutics
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• 제2권1호
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• pp.34-38
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• 1994

In order to investigate the structure-activity relationships of the stereoisomers of angiotensin converting enzyme inhibitors, captopril and its derivatives were selected as model compounds. In vitro enzymatic activities of them depend on the symmetry at the asymmetric carbons. Especially, the alanyl carbon should have the S configuration to be biologically active. But the demethylated captopril having the achiral carbon also shows the activity although it is less active than captopril. Seven stereoisomers of captopril and its derivatives were chosen and their acidic and ionic forms were used for molecular dynamics simulations. Four computer simulations were practiced for each model compound in order to obtain the good condition for simulation to explain the experimental structure-activity relationships. From the computer simulation results, relativistic movements of three well-known pharmacophoric sites, carboxylate carbon, carbonyl oxygen, and sulfur atoms, were analyzed. Good results were obtained from the aqueous solution molecular dynamics simulation with ionic forms of model compounds. Active model compounds have the pharmacophoric areas of 6.08 to 6.38 $\AA$$^2$and the similarity in the geometrical data. But inactive ones have the largely deviated values of 4.51 to 4.87 $\AA$$^2$from those of active ones.

• 한국항공우주학회지
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• 제30권5호
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• pp.15-23
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• 2002

분자 동역학 기법을 사용한 재료 파괴 시뮬레이션은 계산량의 방대함으로 인하여 극히 최근까지 활발한 연구가 진행되지 못하였으나 최근 컴퓨터의 성능향상으로 인하여 새로운 연구분야로 떠오르고 있다. 분자 동역학은 그 특성상 계산 집약적인 환경을 요구함으로 대규모의 연산을 위해서는 슈퍼컴퓨터나 클러스터(cluster)의 사용이 필수적이나 고가의 장비와 사용료로 인하여 많은 제한을 받아왔다. 본 연구에서는 PC를 사용하여 클러스터를 제작하고, 균열이 있는 시편을 사용하여 파괴현상에 대한 분자 수준의 거동을 시뮬레이션 하였으며, 클러스터의 노드(node) 수, 효율, 분자 수, 노드간의 통신시간 등의 상호관계를 파악하여 최적의 성능을 가진 클러스터를 구성하는 데 필요한 요소들을 분석하였다. 제작된 PC 클러스터를 사용하여 약 50,000개의 분자를 사용한 재료 파괴 시뮬레이션을 수행하였다.