• 한국세라믹학회지
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• 제44권5호
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• pp.166-172
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• 2007

In this study, magnetic properties of the strontium ferrite were theoretically investigated by Ab initio (first principle) method. The influences of various additives on the magnetic properties of the strontium ferrite were analyzed to designed new composition of the strontium ferrite system with high magnetic characteristics. As shown in the results, the total magnetization of the strontium ferrite was $42.55M_B$. Based on the DOS results, the magnetic characteristics of the strontium ferrite were mainly influenced by Fe atoms at 6 positions in the unit cell. Also the La-Mn strontium ferrite has the superior magnetic property than the Mn strontium ferrite.

• 한국결정학회지
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• 제2권1호
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• pp.27-31
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• 1991

반경험적인 Tersoff 포텐셜을 사용한 lattice statics 시뮬레이션 테크닉에 의하여 C24와 C60 fullerenes의 구조와 에너지를 구하였다. 그 결과는 ab initio 계산 결과와 잘 일치 하였다.

• 한국재료학회지
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• 제20권9호
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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.

• 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.

• EDISON SW 활용 경진대회 논문집
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• 제3회(2014년)
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• pp.141-155
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• 2014

Peptide bond hydrolysis는 세포 내외의 생화학반응에 있어서 핵심이다. 하지만 amide Hydrolysis Mechanism은 아직 명확하게 규명되지 않았다. pH가 중성인 물에서의 비 촉매 가수분해가 발생하는 몇몇 실험적 증거가 있지만, 해당 반응 매커니즘은 4 가지(non-assisted concerted, non-assisted step-wise, assisted concerted, assisted step-wise)로 여전히 논란이 있다. 이번 연구에서는, Formamide의 가능한 Hydrolysis Mechanism을 자세히 연구해보고자 한다. 먼저, Ab-initio 계산을 통해 4가지 반응 메커니즘의 다시 한번 확인하고, quantum chemical calculations과 quantum mechanical molecular dynamic이 결합된 (QMMD) simulation을 통하여 water solvent에서의 반응 메커니즘의 에너지관계를 규명하였다. 결론적으로 아직 계산이 끝나지 않은 supported concerted mechanism을 제외한 모든 계산에서 non-supported, supported 두 system 모두에서 step-wise가 일어나기 쉬웠고, non-supported 보다 supported mechanism이 선호됨을 보였다. Intermediate인 amino-gem-diol의 수용액 상에서 안정화 또한 나타났다. 이는 Ab-initio 계산만 통해서는 정확하게 산출할 수 없는 엔트로피의 영향을 잘 보여준다.

• EDISON SW 활용 경진대회 논문집
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• 제4회(2015년)
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• pp.91-98
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• 2015

Formamide의 중성가수분해 mechanism은 QM/MM (quantum mecahnics/molecular mechanics) molecular dynamics simulations 및 CPMD과 같은 방법으로 연구되어왔다. 본 연구에서는. Umbrella sampling을 이용한 QM/MM-MD simulation을 사용하여 4가지 반응의 free energy surface를 도출해냈다. 전체적으로, 가장 선호되는 메커니즘은 two step으로 구성된 water assisted stepwise mechanism이었으며 모든 mechanism은 ab-initio calculation과 QM/MM-MD simulation이 수행되었다. water assisted stepwise mechanism을 살펴보면, 첫 번째 step에서 formamide의 carbonyl group이 hydrate되면서 gem-diol intermediate를 형성한다. 다음 step에서, intermediate의 hydroxyl group으로부터 amino group으로 water-assisted proton transfer이 일어난다. 두 반응 모두에서 물이 proton transfer를 직접적으로 도와주는 것을 관찰할 수 있었다. 특히, ab-initio calculation과는 다르게 QM/MM-MD에서는 gem-diol intermediate가 안정화되는 것으로 solvent effect를 잘 보여준다.

• 한국세라믹학회지
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• 제53권3호
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• pp.263-272
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• 2016

Electronic structure calculations have become a powerful foundation for computational materials engineering. Four major factors have enabled this unprecedented evolution, namely (i) the development of density functional theory (DFT), (ii) the creation of highly efficient computer programs to solve the Kohn-Sham equations, (iii) the integration of these programs into productivity-oriented computational environments, and (iv) the phenomenal increase of computing power. In this context, we describe recent applications of the Vienna Ab-initio Simulation Package (VASP) within the MedeA$^{(R)}$ computational environment, which provides interoperability with a comprehensive range of modeling and simulation tools. The focus is on technological applications including microelectronic materials, Li-ion batteries, high-performance ceramics, silicon carbide, and Zr alloys for nuclear power generation. A discussion of current trends including high-throughput calculations concludes this article.

• 한국표면공학회지
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• 제39권2호
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• pp.76-81
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• 2006

Molecular dynamics simulations were carried out to investigate physical sputtering of Fe(100) substrate due to energetic ion bombardments. Repulsive interatomic potentials at short internuclear distances were determined with ab initio calculations using the density functional theory. Bohr potentials were fitted to the ab initio results on diatomic pairs (Ar-Fe, Fe-Fe) and used as repulsive screened Coulombic potentials in sputtering simulations. The fitted-Bohr potentials improve the accuracy of the sputtering yields predicted by molecular dynamics for sputtering of Fe(100), whereas Moliere and ZBL potentials were found to be too repulsive and gave relatively high sputtering yields. In spite of assumptions and limitations in this simulation work, the sputtering yields predicted by the molecular dynamics method were in fairly good accordance with the obtainable experimental data in absolute values as well as in manner of the variation according to the Incident energy. Threshold energy for sputtering of Fe(100) substrate was found to be about 40 eV. Additionally, distributions of kinetic energies of sputtered atoms and their original depths could be obtained.

• 한국신재생에너지학회:학술대회논문집
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• 한국신재생에너지학회 2010년도 추계학술대회 초록집
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• pp.113.2-113.2
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• 2010

We report that the novel covalent organic frameworks (COFs) are capable of reversibly providing an extremely high uptake capacity of carbon dioxide and hydrogen at room temperature. These COFs are designed based on the multiscale simulations approach via the combination of ab initio calculations and force-field calculations. For this goal, we explore the adsorption sites of carbon dioxide and hydrogen on COFs, their porosity, as well as carbon dioxide adsorption isotherms. We identify the binding sites and energies of $CO_2$ on COFs using ab initio calculations and obtain the carbon dioxide adsorption isotherms using grand canonical ensemble Monte Carlo calculations. Moreover, the calculated adsorption isotherms are compared with the experimental values in order to build the reference model in describing the interactions between the $CO_2/H_2$ and the COFs and in predicting the $CO_2$ and $H_2$ adsorption isotherms of COFs. Finally, we design three new COFs, 2D COF-05, 3D COF-05 (ctn), and 3D COF-05 (bor), for the high capacity $CO_2/H_2$ and $H_2$ storage.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.32-34
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• 2000

Computational chemistry is a discipline using computational methods for the calculation of molecular structure, properties, and reaction or for the simulation of molecular behavior. Relating and turning the complexity of data from genomics, high-throughput screening, combinatorial chemical synthesis, gene-expression investigations, pharmacogenomics, and proteomics into useful information and knowledge is the primary goal of bioinformatics. In particular, the structure-based molecular design is one of essential fields in bioinformatics and it can be called as structural bioinformatics. Therefore, the conformational analysis for proteins and peptides using the techniques of computational chemistry is expected to play a role in structural bioinformatics. There are two major computational methods for conformational analysis of proteins and peptides; one is the molecular orbital (MO) method and the other is the force field (or empirical potential function) method. The MO method can be classified into ab initio and semiempirical methods, which have been applied to relatively small and large molecules, respectively. However, the improvement in computer hardwares and softwares enables us to use the ab initio MO method for relatively larger biomolecules with up to v100 atoms or ∼800 basis functions. In order to show how computational chemistry can be used in structural bioinformatics, 1 will present on (1) cis-trans isomerization of proline dipeptide and its derivatives, (2) positional preference of proline in ${\alpha}$-helices, and (3) conformations and activities of Arg-Gly-Asp-containing tetrapeptides.