• 에너지공학
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• 제23권2호
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• pp.7-12
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• 2014

탄소나노튜브의 수소 저장소로써의 가능성을 평가하기 위한 분자 모사를 수행하였다. 일정한 온도와 압력에서 Grand canonical Monte Carlo 방법을 적용하여 탄소나노튜브에 수소가 흡착된 평형 상태를 구현하였다. Lennard-Jones 퍼텐셜 모델로부터 탄소나노튜브와 수소 분자 간 상호 작용 에너지를 계산 한 결과에 의하면 수소 분자는 나노튜브 외부보다 내부에 많은 양이 흡착되는 반면 흡착 강도는 외부가 높은 것으로 나타났다. 여러 가지 온도와 압력에 대해 흡착율을 검토하였으며, 200 K와 200 bar의 저온 고압 조건에서 약 2.5wt%의 흡착율을 나타내었다.

• Genomics & Informatics
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• 제20권3호
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• pp.33.1-33.17
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• 2022

Nervous necrosis virus (NNV) is a deadly infectious disease that affects several fish species. It has been found that the NNV utilizes grouper heat shock cognate protein 70 (GHSC70) to enter the host cell. Thus, blocking the virus entry by targeting the responsible protein can protect the fishes from disease. The main objective of the study was to evaluate the inhibitory potentiality of 70 compounds of Azadirachta indica (Neem plant) which has been reported to show potential antiviral activity against various pathogens, but activity against the NNV has not yet been reported. The binding affinity of 70 compounds was calculated against the GHSC70 with the docking and molecular dynamics (MD) simulation approaches. Both the docking and MD methods predict 4 (PubChem CID: 14492795, 10134, 5280863, and 11119228) inhibitory compounds that bind strongly with the GHSC70 protein with a binding affinity of -9.7, -9.5, -9.1, and -9.0 kcal/mol, respectively. Also, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the compounds confirmed the drug-likeness properties. As a result of the investigation, it may be inferred that Neem plant compounds may act as significant inhibitors of viral entry into the host cell. More in-vitro testing is needed to establish their effectiveness.

• Bulletin of the Korean Chemical Society
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• 제31권6호
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• pp.1519-1526
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• 2010

The behavior of peptide or protein solutes in saline aqueous solution is a fundamental topic in physical chemistry. Addition of ions can strongly alter the thermodynamic and physical properties of peptide molecules in solution. In order to study the effects of added ionic salts on protein conformation and dynamics, we have used the molecular dynamics (MD) simulations to investigate the behavior of Staphylococcus aureus Hfq protein under two different ionic concentrations: 0.1 M NaCl and 1.0 M NaCl in presence and absence of RNA (a hepta-oligoribonucleotide AU5G). Hfq, a global regulator of gene expression is highly conserved and abundant RNA-binding protein. It is already reported that in vivo the increase of ionic strength results in a drastic reduction of Hfq affinity for $Q{\beta}$ RNA and reduces the tendency of aggregation of Escherichia coli host factor hexamers. Our results revealed the crucial role of 0.1 M NaCl Hfq system on the bases with strong hydrogen bonding interactions and by stabilizing the aromatic stacking of Tyr42 residue of the adjacent subunits/monomers with the adenine and uridine nucleobases. An increase in RNA pore diameter and weakened compactness of the Hfq-RNA complex was clearly observed in 1.0 M NaCl Hfq system with bound RNA. Aggregation of monomers in Hfq and the interaction of Hfq with RNA are greatly affected due to the presence of high ionic strength. Higher the ionic concentration, weaker is the aggregation and interaction. Our results were compatible with the experimental data and this is the first theoretical report for the experimental study done in 1980 by Uhlenbeck group for the present system.

• Bulletin of the Korean Chemical Society
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• 제33권3호
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• pp.869-880
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• 2012

Identification of the selective chemical features for Aurora-B inhibitors gained much attraction in drug discovery for the treatment of cancer. Hence to identify the Aurora-B critical features various techniques were utilized such as pharmacophore generation, virtual screening, homology modeling, molecular dynamics, and docking. Top ten hypotheses were generated for Aurora-B and Aurora-A. Among ten hypotheses, HypoB1 and HypoA1 were selected as a best hypothesis for Aurora-B and Aurora-A based on cluster analysis and ranking score, respectively. Test set result revealed that ring aromatic (RA) group in HypoB1 plays an essential role in differentiates Aurora-B from Aurora-A inhibitors. Hence, HypoB1 used as 3D query in virtual screening of databases and the hits were sorted out by applying drug-like properties and molecular docking. The molecular docking result revealed that 15 hits have shown strong hydrogen bond interactions with Ala157, Glu155, and Lys106. Hence, we proposed that HypoB1 might be a reasonable hypothesis to retrieve the structurally diverse and selective leads from various databases to inhibit Aurora-B.

• Molecules and Cells
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• 제39권4호
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• pp.316-321
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• 2016

The receptor activator of nuclear factor ${\kappa}B$ (RANK) and its ligand RANKL are key regulators of osteoclastogenesis and well-recognized targets in developing treatments for bone disorders associated with excessive bone resorption, such as osteoporosis. Our previous work on the structure of the RANK-RANKL complex revealed that Loop3 of RANK, specifically the non-canonical disulfide bond at the tip, performs a crucial role in specific recognition of RANKL. It also demonstrated that peptide mimics of Loop3 were capable of interfering with the function of RANKL in osteoclastogenesis. Here, we reported the structure-based design of a smaller peptide with enhanced inhibitory efficiency. The kinetic analysis and osteoclast differentiation assay showed that in addition to the sharp turn induced by the disulfide bond, two consecutive arginine residues were also important for binding to RANKL and inhibiting osteoclastogenesis. Docking and molecular dynamics simulations proposed the binding mode of the peptide to the RANKL trimer, showing that the arginine residues provide electrostatic interactions with RANKL and contribute to stabilizing the complex. These findings provided useful information for the rational design of therapeutics for bone diseases associated with RANK/RANKL function.

• 광물과 암석
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• 제33권3호
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• pp.143-152
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• 2020

버네사이트(birnessite)는 약 7Å의 d-spacing을 가지는 대표적인 층상형 산화망간광물로 높은 양이온 교환능력을 가지기 때문에 지하수나 퇴적물 공극 유체의 화학조성을 결정짓는 중요한 역할을 한다. 버네사이트의 양이온 교환 반응 기작을 규명하기 위해서는 층간 내 양이온의 배위 환경과 결정구조에 대한 원자 수준의 이해가 매우 중요하다. 이번 연구에서는 원자 수준의 계산광물학 방법인 고전 분자동역학(classical molecular dynamics; MD) 시뮬레이션을 이용하여 기존 실험에서 보고된 화학조성을 가지는 삼사정계 Na-와 K-버네사이트의 결정구조, 층간 양이온의 배위 환경 및 적층 구조를 계산하였다. 계산 결과는 기존 X-선 실험에서 보고된 격자 상수와 층간 배위 환경을 잘 재현하여 시뮬레이션 방법의 신뢰성을 보여주었으며, X-선 실험만으로는 구분하기 어려운 층간의 양이온과 물 분자 위치를 구별한 원자 수준의 정보를 제공하였다. 망간 팔면체 층의 적층 순서는 동일하지만 층간 내 Na⁺와 K⁺의 위치가 서로 상이하고, 층간 양이온의 배위 환경과 결정구조 간의 상관관계를 보인다. 원자 수준의 분자동역학 시뮬레이션은 버네사이트의 양이온 교환 반응 기작 규명에 크게 기여할 것으로 기대한다.

• 한국진공학회지
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• 제15권4호
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• pp.410-420
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• 2006

Epitaxial 성장에서 screening 및 steering 효과 등과 같은 증착과정 중 나타나는 dynamic effects를 kinetic Monte Carlo 시뮬레이션으로 고찰하였다. 증착원자와 토대 원자와의 상호 작용을 엄밀하게 고려하기 위해 이 시뮬레이션 프로그램에 molecular dynamics 시뮬레이션을 결합시켰다. 기울어진 각도로 증착 시킬 경우 표면의 형상은 1) 증착 각도가 기울어짐에 따라 거칠기가 증가한다는 것, 2) 비대칭적인 언덕의 형성된다는 것, 그리고 3) 언덕의 면방향에 따라 비대칭적인 기울기를 갖는다는 세가지 특징을 보았다. 증착 각도나 온도 의존성에 대한 시뮬레이션 결과는 기존의 실험 결과와 잘 일치하는 것을 확인하였다. 기울어진 각도로 증착했을 때 나타나는 이러한 결과는 steering과 screening 효과에 따른 초기 증착 밀도의 불균일에 기인함을 알 수 있었고, 여기서 steering 효과가 screening 효과 보다 주요한 역할을 하는 것을 보았다. 시뮬레이션 계산에서 확인된 새로운 결과는 기울기 선택 (slope selection)이 이루어졌어도 언덕의 각 면이 단일한 기울기로 형성되어 있지 않고 여러 종류의 facet가 섞인 형태이며, 따라서 기울기 선택이 바로 facet 선택을 의미하지는 않는다는 것이다.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제40회 동계학술대회 초록집
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• pp.428-429
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• 2011

Recently, we performed ab initio total energy calculation and tight-binding molecular dynamics (TBMD) simulation to study structures and the reconstruction of native defects in graphene. In the previous study, we predicted by TBMD simulation that a double vacancy in graphene is reconstructed into a 555-777 composed of triple pentagons and triple heptagons [1]. The structural change from pentagon-octagon-pentagon (5-8-5) to 555-777 has been confirmed by recent experiments [2,3] and the detail of the reconstruction process is carefully studied by ab initio calculation. Pentagon-heptagon (5-7) pairs are also found to play an important role in the reconstruction of vacancy in graphene and single wall carbon nanotube [4]. In the TBMD simulation of graphene nanoribbon (GNR), we found the evaporation of carbon atoms from both the zigzag and armchair edges is preceded by the formation of heptagon rings, which serve as a gateway for carbon atoms to escape. In the simulation for a GNR armchair-zigzag-armchair junction, carbon atoms are evaporated row-by-row from the outermost row of the zigzag edge [5], which is in excellent agreement with recent experiments [2, 6]. We also present the recent results on the formation and development of dislocation in graphene. It is found that the coalescence of 5-7 pairs with vacancy defects develops dislocation in graphene and induces the separation of two 5-7 pairs. Our TBMD simulations also show that adatoms are ejected and evaporated from graphene surface due to large strain around 5-7 pairs. It is observed that an adatom wanders on the graphene surface and helps non-hexagonal rings change into stable hexagonal rings before its evaporation.

• 한국전기전자재료학회논문지
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• 제19권2호
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• pp.195-199
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• 2006

We report a novel simulation method to calculate optical transmission considering the real paths of optic introduced in a unit pixel of TFT-LCDs using three-dimensional molecular director simulation of the tensor model. The simulation of optical path transmission profile was carried out by calculating new permittivity considered the real paths of optic in liquid crystal cell. As a result, it was clarified that the electro-optic characteristics such as movement of disclination line, contrast ratio and transmittance profile show a large difference according to the viewing angle compared with the conventional method.

• 반도체디스플레이기술학회지
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• 제11권1호
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• pp.49-54
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• 2012

There have been plenty of difficulties because properties of Alq3 are unable to acquire in a process of manufacture of OLED. In this paper it will predict a viscosity of Alq3 through DSMC technique and suggest the way regarding a study to estimate properties of material through the computer simulation. There could generate errors of a simulation process in a vacuum deposition process since the properties of material that is used in a high-degree vacuum environment are not secured. Therefore, we would like to propose the new methods that can not only predict properties of a molecular unit but also raise an accuracy of simulation process by forecasting properties of Alq3.