• Microbiology and Biotechnology Letters
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• v.46 no.3
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• pp.300-312
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• 2018

Whole-genome sequencing of the wood-rotting fungus, Flammulina fennae, was carried out to identify carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) of short reads by next-generation sequencing revealed a total genome length of 32,423,623 base pairs (39% GC). A total of 11,591 gene models in the assembled genome sequence of F. fennae were predicted by ab initio gene prediction using the AUGUSTUS tool. In a genome-wide comparison, 6,715 orthologous groups shared at least one gene with F. fennae and 10,667 (92%) of 11,591 genes for F. fennae proteins had orthologs among the Dikarya. Additionally, F. fennae contained 23 species-specific genes, of which 16 were paralogous. CAZyme identification and annotation revealed 513 CAZymes, including 82 auxiliary activities, 220 glycoside hydrolases, 85 glycosyltransferases, 20 polysaccharide lyases, 57 carbohydrate esterases, and 45 carbohydrate binding-modules in the F. fennae genome. The genome information of F. fennae increases the understanding of this basidiomycete fungus. CAZyme gene information will be useful for detailed studies of lignocellulosic biomass degradation for biotechnological and industrial applications.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2006.11a
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• pp.201-201
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• 2006

영구자석은 크게 Hard ferrite와 희토류계 자석, 그리고 Alnico 주조자석으로 구별되어진다. 그동안 Hard ferrite는 산업적으로 전자기 응용제품 또는 각종 구동 모터에 응용되어 왔지만, 최근 Nd계 희토류 자것이 고성능 모터의 소재로 급격히 대체되고 있다. 하지만, 희토류계 원료에 비해 동일 중량 대비 40~60배 가량 저렴한 Hard ferrite의 사용은 현재까지도 꾸준히 유지되고 있으며, 최근 자동차 고성능 모터용 Sr ferrite의 개발이 연구 중이다.[2] 본 연구에서는 제일원리 전산모사를 통하여 HCP 구조의 기본 Unit Cell 64개 원자를 가진 Sr-ferrite의 격자상수를 계산하여 기존 연구결과와 비교하였으며, 자화에너지와 자기모멘트를 계산하였다. 또한 향후 각종 첨가물의 영향에 대한 연구를 위해 기본 구조 및 치환 구조에 대해 고찰하였다. 그 결과 가장 안정한 에너지를 갖는 격자상수는 a=5.88, b=23.03으로 계산되어 Kimura et al의 측정 결과와 유사한 결과를 얻을 수 있었으며, $E_F$가 3.9171, $M_B$는 46.6481로 계산되었다. 항후 Sr-ferrite의 구조에서 Fe atom의 일부를 동일주기 원소인 Cr, Mn, Co, Ni, Cu로 치환하여 자기적 특성을 계산하여 본 연구결과와 비교하고자 한다.

• Journal of the Semiconductor & Display Technology
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• v.7 no.3
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• pp.35-39
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• 2008

We study the interaction of acetone molecule $[(CH_3)_2CO]$ on Si(001) surface using density functional theory. An acetone molecule is adsorbed on a Si atom of the Si dimer of the Si(001) surface. The adsorption of the acetone molecule on the Si atom at lower height between the two Si atoms of the dimer is more favorable than that on the Si atoms at upper height. Then we calculate an energy variation of dissociation and four-membered ring structures of the acetone molecule adsorbed on the Si surface. Total energy difference between the two structures is about 0.05 eV, indicating that the two structures are almost equally stable. Energy barrier exists when a hydrogen atom is dissociated and adsorbed on the other Si atom of the dimer, while energy barrier does not exist when the adsorbed acetone molecule changes to four-membered ring structure, except for the rotation of the acetone molecule along z-direction. Therefore, four-membered ring structure is kinetically more favorable than the dissociation structure when the acetone molecule is adsorbed on the Si(001) surface.

• Journal of the Korean Chemical Society
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• v.41 no.3
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• pp.123-129
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• 1997

In order to consider the reduced mass effects on the out-of-plane ring inversion vibration of 1,3-CHD, the vector-based computer program has been written and the kinetic energy expansion function for the large amplitude ring inversion vibration has been calculated using this program. The structural parameters for the calculations have been determined from the ab initio HF/6-31G** calculation. The potential energy function for the out-of-plane ring inversion vibration of 1,3-CHD has been determined from the kinetic energy expansion function and previously reported low-frequency Raman data. The vibrational Hamiltonian calculation including kinetic energy expansion function made it possible to determine the more reliable out-of-plane potential energy function for the ring inversion of 1,3-CHD.

• Genomics & Informatics
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• v.11 no.3
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• pp.155-160
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• 2013

Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.18 no.7
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• pp.589-593
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• 2005

The electronic states of ZnO doped with Al, Ga and In, which belong to III family elements in periodic table, were calculated using the density functional theory. In this study, the calculation was performed by two Programs; the discrete variational Xa (DV-Xa) method, which is a sort of molecular orbital full potential method; Vienna Ab-initio Simulation Package (VASP), which is a sort of pseudo potential method. The fundamental mixed orbital structure in each energy level near the Fermi level was investigated with simple model using DV-Xa. The optimized crystal structures calculated by VASP were compared to the measured structures. The density of state and the energy levels of dopant elements were shown and discussed in association with properties.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.250-261
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• 2004

A novel method for ab initio prediction of protein tertiary structures, PROFESY (PROFile Enumerating SYstem), is introduced. This method utilizes secondary structure prediction information and fragment assembly. The secondary structure prediction of proteins is performed with the PREDICT method which uses PSI-BLAST to generate profiles and a distance measure in the pattern space. In order to predict the tertiary structure of a protein sequence, we assemble fragments in the fragment library constructed as a byproduct of PREDICT. The tertiary structure is obtained by minimizing the potential energy using the conformational space annealing method which enables one to sample diverse low lying minima of the energy function. We apply PROFESY for prediction of some proteins with known structures, which shows good performances. We also participated in CASP5 and applied PROFESY to new fold targets for blind predictions. The results were quite promising, despite the fact that PROFESY was in its early stage of development. In particular, the PROFESY result is the best for the hardest target T0161.

• Bulletin of the Korean Chemical Society
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• v.25 no.5
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• pp.704-710
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• 2004

A poly(1-hexyl-3,4-dimethyl-2,5-pyrrolylene) (PHDP) was prepared and its luminescence in tetrahydrofuran (THF) was studied. When PHDP is excited by UV light, it produces very strong blue luminescence. The quantum yield of PHDP (Q = 36.9%) is much greater than that of the monomer, 1-hexyl-3,4-dimethylpyrrole (HDP) with Q = 0.61%. The principal luminescence of PHDP has a single decay component with ca. 1 ns, whereas the decay of HDP is complicated. The molecular structure and conformational behavior of HDP and the oligomers up to trimer have been also determined by ab initio Hartree-Fock (HF/6-31$G^{**}$), density functional theory (DFT-B3LYP/6-31$G^{**}$), and semiempirical (ZINDO) methods. According to the results of calculations, it is proposed that the enhanced quantum yield of the polymer PHDP results mostly from the ${\pi}$-conjugation between neighboring pyrrole rings.

• Mass Spectrometry Letters
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• v.4 no.4
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• pp.67-70
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• 2013

The Cu-binding site in the $[Cu{\cdot}dCMP{\cdot}dCMP-H]^{1-}$ complex was investigated. The tandem mass (MS/MS) spectra of the [$[Cu{\cdot}dCMP{\cdot}dCMP-H]^{1-}$ parent ion showed $[dCMP{\cdot}Cu{\cdot}H_2PO_4+CONH]^{1-}$ fragment ions. Therefore, we propose that the Cu cation is simultaneously coordinated to the phosphate site and cytosine moiety in the stable geometry of the $[Cu{\cdot}dCMP{\cdot}dCMP-H]^{1-}$ complex. Three geometries for the complex were considered in an attempt to optimize the structure of the $[Cu{\cdot}dCMP{\cdot}dCMP-H]^{1-}$ complex. The ab initio calculations were performed at the $B3LYP/6-311G^{**}$ level.

• Journal of the Korean Crystal Growth and Crystal Technology
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• v.17 no.5
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• pp.192-195
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• 2007

Structural and electronic properties of bulk GaN with nitrogen vacancy($V_N$), oxygen substitution on nitrogen site($O_N$), and complex of nitrogen vacancy and oxygen substitution on nitrogen site($V_N-O_N$) were investigated using the first principle calculations. It was found that stability of defect formation is dependent on the epilayer growth conditions. The complex of $V_N-O_N$ is energetically the most favorable state in a condition of Ga-rich, however, oxygen substitution in nitrogen site is the most favorable state in N-rich condition. The electronic property of complex with negative charge states at $\Gamma$ point was changed from semiconductor to metal. On the contrary, the properties of nitrogen vacancy except for neutral charge state have shown the semiconductor characteristics at $\Gamma$ point. In the oxygen substitution on nitrogen site, the energy differences between conduction band minimum and Fermi level were smaller than that of defect-free GaN.