• Bulletin of the Korean Chemical Society
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• v.14 no.3
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• pp.356-362
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• 1993

• Applied Chemistry for Engineering
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• v.18 no.6
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• pp.643-649
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• 2007

Lipase-catalyzed esterification of structural butanol isomers and n-butyric acid was investigated in supercritical carbon dioxide. The experiments were performed in a high pressure cell for 5 hrs with a stirring rate of 150 rpm at 323.15 K and 130 bar. The Candida Antarctica lipase B (CALB) was used in whole system as a catalyst. The experimental results were analyzed by GC-FID using a INNOWax capillary column. The conversion yield and the tendency of the esterification in supercritical carbon dioxide were compared with estimated results by molecular dynamics simulation. Based on the Ping-Pong Bi-Bi mechanism with competitive inhibition, each step of the reaction was optimized; using this result the transition state was predicted. Conformational preference of isomers was also analyzed using molecular dynamics simulations. This kind of approach will be further extended to the prediction of enzyme-catalyzed reactions using computers.

• Bulletin of the Korean Chemical Society
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• v.26 no.5
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• pp.769-775
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• 2005

An efficiency of Monte Carlo (MC) docking simulations was examined for the prediction of chiral discrimination by cyclodextrins. Docking simulations were performed with various computational parameters for the chiral discrimination of a series of 17 enantiomers by $\beta$-cyclodextrin ($\beta$-CD) or by 6-amino-6-deoxy-$\beta$-cyclodextrin (am-$\beta$-CD). A total of 30 sets of enantiomeric complexes were tested to find the optimal simulation parameters for accurate predictions. Rigid-body MC docking simulations gave more accurate predictions than flexible docking simulations. The accuracy was also affected by both the simulation temperature and the kind of force field. The prediction rate of chiral preference was improved by as much as 76.7% when rigid-body MC docking simulations were performed at low-temperatures (100 K) with a sugar22 parameter set in the CHARMM force field. Our approach for MC docking simulations suggested that the conformational rigidity of both the host and guest molecule, due to either the low-temperature or rigid-body docking condition, contributed greatly to the prediction of chiral discrimination.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.848-854
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• 2012

We have studied the oligomerization of a fibril-forming segment of ${\alpha}$-Synulcein using a replica exchange molecular dynamics (REMD) simulation. The simulation was performed with trimers and tetramers of a 12 amino acid residue stretch (residues 71-82) of ${\alpha}$-Synulcein. From extensive REMD simulations, we observed the spontaneous formation of both trimer and tetramer, demonstrating the self-aggregating and fibril-forming properties of the peptides. Secondary structure profile and clustering analysis illustrated that antiparallel ${\beta}$-sheet structures are major species corresponding to the global free energy minimum. As the size of the oligomer increases from a dimer to a tetramer, conformational stability is increased. We examined the evolution of simple order parameters and their free energy profiles to identify the process of aggregation. It was found that the degree of aggregation increased as time passed. Tetramer formation was slower than trimer formation and a transition in order parameters was observed, indicating the full development of tetramer conformation which is more stable than that of the trimer. The shape of free energy surface and change of order parameter distributions indicate that the oligomer formation follows a dock-and-lock process.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.1
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• pp.24-29
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• 2014

Atomistic molecular dynamics (MD) simulation has become mature enabling close approximation of the real behaviors of biomolecules. In biomolecular NMR field, atomistic MD simulation coupled with generalized implicit solvent model (GBIS) has contributed to improving the qualities of NMR structures in the refinement stage with experimental restraints. Here all-atom force fields play important roles in defining the optimal positions between atoms and angles, resulting in more precise and accurate structures. Despite successful applications in refining NMR structure, however, the research that has studied the influence of force fields in GBIS is limited. In this study, we compared the qualities of NMR structures of two model proteins, ubiquitin and GB1, under a series of AMBER force fields-ff99SB, ff99SB-ILDN, ff99SB-NMR, ff12SB, and ff13-with experimental restraints. The root mean square deviations of backbone atoms and packing scores that reflect the apparent structural qualities were almost indistinguishable except ff13. Qualitative comparison of parameters, however, indicates that ff99SB-ILDN is more recommendable, at least in the cases of ubiquitin and GB1.

• Korean Journal of Materials Research
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• v.20 no.9
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• pp.478-482
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• 2010

A series of molecular dynamic (MD), finite element (FE) and ab initio simulations are carried out to establish suitable modeling schemes for the continuum-based analysis of aluminum matrix nanocomposites reinforced with carbon nanotubes (CNTs). From a comparison of the MD with FE models and inferences based on bond structures and electron distributions, we propose that the effective thickness of a CNT wall for its continuum representation should be related to the graphitic inter-planar spacing of 3.4${\AA}$. We also show that shell element representation of a CNT structure in the FE models properly simulated the carbon-carbon covalent bonding and long-range interactions in terms of the load-displacement behaviors. Estimation of the effective interfacial elastic properties by ab initio simulations showed that the in-plane interfacial bond strength is negligibly weaker than the normal counterpart due to the nature of the weak secondary bonding at the CNT-Al interface. Therefore, we suggest that a third-phase solid element representation of the CNT-Al interface in nanocomposites is not physically meaningful and that spring or bar element representation of the weak interfacial bonding would be more appropriate as in the cases of polymer matrix counterparts. The possibility of treating the interface as a simply contacted phase boundary is also discussed.

• Proceedings of the IEEK Conference
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• 1999.11a
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• pp.895-898
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• 1999

We calculated Al-Absorption, Al-reflection, and Si-etching probabilities as a function of incident angle and energy using classical molecular dynamics (MD) simulation. Variations of the cases of Al-absorption rate and Al-reflection rate are less than that of Si-etching rate. In contrast with general prediction, our simulation results showed that channeling of the <110> direction occurred the most in the case of incident angle between 30degree and 40degree. We investigated that channeling of the <110> directions quite affect Al-absorption rate in silicon. Since Si-etching rate is high and Al-absorption rate by <110> channeling is high, we found that Al ionized physical vapor deposition (PVD) on Si(001) has a different characteristics with Al ionized PVD on A1(111).

• Genomics & Informatics
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• v.6 no.2
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• pp.72-76
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• 2008

Hypoxia-inducible factor $1{\alpha}\;(HIF1{\alpha})$ is a transcription factor that plays a key role in the adaptation of cells to low oxygen stress and oxygen homeostasis. The oxygen-dependent degradation (ODD) domain of $HIF1{\alpha}$ is responsible for the negative regulation of $HIF1{\alpha}$ in normoxia. The interactions of the $HIF1{\alpha}$ ODD domain with partner proteins such as von Hippel-Lindau tumor suppressor (pVHL) and p53 are mediated by two sequence motifs, the N- and C-terminal ODD(NODD and CODD). Multiple sequence alignment with $HIF1{\alpha}$ homologs from human, monkey, pig, rat, mouse, chicken, frog, and zebrafish has demonstrated that the NODD and CODD motifs have noticeably high conservation of the primary sequence across different species and isoforms. In this study, we carried out molecular dynamics simulation of the structure of the $HIF1{\alpha}$ CODD motif in complex with the p53 DNA-binding domain (DBD). The structure reveals specific functional roles of highly conserved residues in the CODD sequence motif of $HIF1{\alpha}$ for the recognition of p53.

• Proceedings of the Korean Information Science Society Conference
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• 2007.06b
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• pp.358-362
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• 2007

Glycomics와 Glycobiology는 Oligosaccharides와 Carbohydrate의 구조와 기능을 연구하기 위한 중요한 연구 방법이다. 현재 컴퓨터 시뮬레이션을 이용한 분자 모사 실험이 많은 연구 단체에 의해서 진행되고 있지만, 많은 컴퓨터 자원을 요구하는 문제로 인해서 활발하게 이루어 지지 않고 있는 실정이다. 현 시점에서 이러한 문제를 해결하기 위해서는 많은 자원과 오랜 시간을 소비해서 얻은 결과 데이터를 많은 과학자들에 의해서 공유하고 협업할 수 있는 시스템이 필요하다. Glyco-MGrid시스템은 분자 시뮬레이션 서비스 제공에 중점을 두고 있는 MGrid에서 생성되는 e-Clycomics 데이터들을 통합 관리하기 위한 사이버인프라스트럭쳐이다. 이 Glyco-MGrid는 분자 시뮬레이션의 결과를 통합 관리하기 위한 통합 데이터베이스 제공과 이를 통한 과학자들간의 협업을 지원하기 위해 그리드 기반의 e-Glycomics를 위한 공유, 통합 환경을 제공한다.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.08a
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• pp.54-55
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• 2010

Vacancy defects in graphene can be created by electron or ion irradiation and those induce ripples which can change the electronic properties of graphene. Recently, the formation of defect structures such as vacancy defects and non-hexagonal rings has been reported in the high resolution transmission electron microscope (HR-TEM) of reduced graphene oxide [1]. In those HR-TEM images, it is noticed that the dislocations with pentagon-heptagon (5-7) pairs are formed and diffuses. Interestingly, it is also observed that two 5-7 pairs are separated and diffuse far away from each other. The separation of 5-7 pairs has been known to be due to their self-diffusion. However, from our tight-binding molecular dynamics simulation, it is found that the separation of 5-7 pairs is due to the diffusion of single vacancy defects and coalescence with 5-7 pairs. The diffusion and coalescence of single vacancy defects is too fast to be observed even in HR-TEM. We also implemented Van der Waals interaction in our tight-binding carbon model to describe correctly bi-layer and multi-layer graphene. The compressibility of graphite along c-axis in our tight-binding calculation is found to be in excellent agreement with experiment. We also discuss the difference between single layer and bi-layer graphene about vacancy diffusion and reconstruction.