• ALGAE
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• v.24 no.3
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• pp.129-138
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• 2009

DNA-based discrimination of species is a powerful way for morphologically otherwise similar species, like centric diatoms. Here, the author sequenced long-range nuclear ribosomal DNAs, spanning from the 18S to the D5 region of the 28S rDNA, of Stephanodiscus, particularly including a Korean isolate. By comparisons, high DNA similarities were detected from the rDNAs of nine Stephanodiscus (>99.4% in 18S rDNA, >98.0% in 28S rDNA). Their genetic distances, however, were significantly different (Kruskal-Wallis test, p < 0.01) compared to two related genera, namely Cyclotella and Discostella. In addition, genetic distances of 18S rDNAs were significantly different (Student’s t-test, p = 0.000) against those of the 28S rDNAs according to individual genera (Cyclotella, Discostella, and Stephanodiscus). Phylogenetic analyses showed that Stephanodiscus and Discostella showed a sister taxon relationship, and their clade was separated from a cluster of Cyclotella (1.00 PP, 100% BP). This suggests that Stephanodiscus has highly conserved sequences of both 18S and 28S rDNA; however, Stephanodiscus is well-separated from other freshwater centric diatoms, such as Cyclotella and Discostella, at the generic level.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2003.07a
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• pp.259-262
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• 2003

The surface electronic state of rutile $TiO_2$, which is an oxide semiconductor and has a wide band gap of 3.1 $\sim$ 3.5 eV, was calculated by DV-$X_{\alpha}$ method, which is a sort of the first principle molecular orbital method and uses Hartre-Fock-Slater approximation. The $[Ti_{15}O_{56}]^{-52}$ cluster model was used for the calculation of bulk state and the $[OTi_{11}O_{34}]^{-24}$ model for the surface state calculation. After calculations, the energy level diagrams and the deformation electron density distribution map were compared in both models. As results, it was identified that the surface energy levels are found between the valence and conduction band of bulk $TiO_2$ on the surface area. The energy values of these surface-induced levels are lower than conduction band of bulk $TiO_2$ by 0.1 $\sim$ 1 eV. From this fact, it is expected that the surface energy levels act as donar levels in n-type semiconductor.

• Bulletin of the Korean Chemical Society
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• v.26 no.1
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• pp.119-126
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• 2005

The geometrical parameters, vibrational frequencies, and relative energies of H$_2$(A$_{n+1}$X$_{2n}$)H$_2$ (A=C or Si, X=O or S, n = 1-2) oligomers have been investigated using high level ab initio quantum mechanical techniques with large basis sets. The equilibrium geometries have been optimized at the self-consistent field (SCF), the coupled cluster with single and double excitation (CCSD), and the CCSD with connected triple excitations [CCSD(T)] levels of theory. The highest level of theory employed in this study is cc-pVTZ CCSD(T). Harmonic vibrational frequencies and IR intensities are also determined at the SCF level of theory with various basis sets and confirm that all the optimized geometries are true minima. Also zero-point vibrational energies have been considered to predict the dimerization and the relative energies.

• Korean Journal of Materials Research
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• v.12 no.4
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• pp.274-278
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• 2002

Discrete-variational(DV)-$X{\alpha}$ method was applied to investigate the electronic structures of spinel- type manganese oxide which is well known to the high performance adsorbent or cathode material for lithium ion. The results of DOS(density of states) and Mulliken population analysis showed that Li was nearly fully ionized and interactions between Mn and O were strong covalent bond. The effective charge of Li and Mn was +0.77 and +1.44 respectively and the overlap population between Mn and O was 0.252 in $LiMn_2O_4$. These results from DV-X$\alpha$ method were well coincided with the experimental result by XPS analysis and supported the feasibility of theoretical interpretation for the $LiMn_2O_4$ compound.

• Fisheries and Aquatic Sciences
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• v.12 no.1
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• pp.54-59
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• 2009

Carotenoids such as $\beta$-carotene and astaxanthin are used as food colorants, animal feed supplements and for nutritional and cosmetic purposes. In a previous study, an astaxanthin biosynthesis gene cluster was isolated from the marine bacterium, Paracoccus haeundaensis. Geranylgeranyl pyrophosphate (GGPP) synthase (CrtE), encoded by the ortE gene, catalyzes the formation of GGPP from farnesyl pyrophosphate (FPP), which is an essential enzyme for the biosynthesis of carotenoids in early steps. In order to study the biochemical and enzymatic characteristics of this important enzyme, a large quantity of purified GGPP synthase is required. To overproduce GGPP synthase, the crtE gene was subcloned into a pET-44a(+) expression vector and transformed into the Escherichia coli BL21(DE3) codon plus cell. Transformants harboring the crtE gene were cultured and the crtE gene was over-expressed. The expressed protein was purified to homogeneity by affinity chromatography and applied to study its biochemical properties and molecular characteristics.

• Korean Journal of Crystallography
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• v.14 no.1
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• pp.16-23
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• 2003

The electronic structure and chemical bonding of β-MnO₂ were theoretically investigated by DV-X/sub α/ (the discrete variation X/sub α/) method. which is a sort of the first principle molecular orbital method using Hatre-Fock-Slater approximation. The calculations on several cluster models having different sizes were carried out for the determination of a model suited for analyzing bulk state. The Mn/sub 15/O/sub 56/ model was selected as a sufficiently suitable model for the calculation of electronic state and chemical bonding by the comparison of the calculated XPS (X-ray photo-electron spectrum) and experimentally measured XPS. By using this model, the electron energy level, the density of state, the bond overlap population, the charge density distribution, and the net ionic transfer between cations and anions were calculated and discussed.

• Bulletin of the Korean Chemical Society
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• v.33 no.11
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• pp.3719-3726
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• 2012

Formation of Z-DNA, a left-handed double helix, from B-DNA, the canonical right-handed double helix, occurs during important biological processes such as gene expression and DNA transcription. Such B-Z transitions can also be induced by high salt concentration in vitro, but the changes in the relative stability of B-DNA and Z-DNA with salt concentration have not been fully explained despite numerous attempts. For example, electrostatic effects alone could not account for salt-induced B-Z transitions in previous studies. In this paper, we propose that the B-Z transition can be explained if counterion entropy is considered along with the electrostatic interactions. This can be achieved by conducting all-atom, explicit-solvent MD simulations followed by MM-PBSA and molecular DFT calculations. Our MD simulations show that counterions tend to bind at specific sites in B-DNA and Z-DNA, and that more ions cluster near Z-DNA than near B-DNA. Moreover, the difference in counterion ordering near B-DNA and Z-DNA is larger at a low salt concentration than at a high concentration. The results imply that the exclusion of counterions by Z-DNA-binding proteins may facilitate Z-DNA formation under physiological conditions.

• International Journal of Ocean System Engineering
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• v.3 no.2
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• pp.102-110
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• 2013

The purpose of this study was to improve the properties of epoxy resin using titanium oxide nanoparticles. The effects of particle weight fraction, dispersion agent, and curing agents with different molecular weights on the thermal and mechanical properties of titanium-oxide-reinforced epoxy resin were investigated. In addition, the effect of the particle dispersion condition on the mechanical properties of nanocomposites was studied. As a result, it was found that the glass transition temperature of film-shaped nanocomposites decreased with an in-crease in the nanoparticle content. Because nanoparticles interrupted the cross linkage between the epoxy resin and the amine curing agent, the cross-link density of the epoxy became lower and led to a decrease in $T_g$ in the nanocompo-sites. The tensile strength and modulus in film-shaped nanocomposites also increased with the particles content. But in the case of dog-bone-shaped nanocomposites, the values were not similar to the trend for the film-shaped nanocompo-sites. This was probably a result of the different nanoparticles dispersions in the epoxy resins resulting from the respective-thicknesses of the film and dog-bone-shaped samples.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2003.11a
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• pp.99-102
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• 2003

The electronic structure of ${\beta}-MnO_2$ having impurities in the site of Mn was theoretically investigated by $DV-X_{\alpha}$ (the discrete variation $X{\alpha}$) method, which is a sort of the first principle molecular orbital method using Hatre-Fock-Slater approximation. The used cluster model was $[Mn_{14}MO_{56}]^{-52}$ (M = transient metals). Madelung potential and spin polarization were considered for more exact calculations. As results of calculations, the energy levels of all electron included in the model were obtained. The energy band gap and positions of impurity levies were discussed in association with impurity 34 orbital that seriously affect electrical properties of $MnO_2$. It was shown that the energy band gap decreased with the increase of the atomic number of transient metal impurity.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2004.07a
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• pp.309-312
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• 2004

The electronic structure of ZnO oxide semiconductor having high optical transparency and good electric conductivity was theoretically investigated by $DV-X_{\alpha}$(the discrete variation $X_{\alpha}$) method, which is a sort of the first principle molecular orbital method using Hatre-Fock-Slater approximation. The electrical and optical properties of ZnO are seriously affected by the addition of impurities. The imnurities are added to ZnO in order to increase the electric conductivity of an electrode without losing optical transparency. In this study, the effect of impurities of III and IV family on the band structure, impurity levels and the density of state of ZnO were investigated. The cluster model used for calculations was $[MZn_{50}O_{53}]^{-2}$(M=elements belonging to III and IV family).