• Genomics & Informatics
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• v.8 no.2
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• pp.70-75
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• 2010

Asp66his, Asp54Lys, and Asp50Asn are mutations in connexin 26 that are observed in the clinic and give rise to autosomal dominant syndromes. They are the result of point mutations in the human gap junction ${\beta}-2$ gene. In order to investigate the structural mechanism of Bart-Pumphrey Syndrome, Keratitis-Ichthyosis-Deafness Syndrome, and Vohwinkel Syndrome, homology modeling was carried out. Asp66 has direct contact with Asn62 by two hydrogen bonds in the wild-type protein, and in Asp66His, the biggest change observed is a tremendous energy increase caused by hydrogen bond breakage to Asn62. Shifts in the side chain and new hydrogen bond formation are observed for Lys54 compared to the wild-type protein (Asn54) and result in closer contact to Val84. Asp50Asn causes a significant decrease in bond energy, and residual charge reversal repels the ion and metabolites and, hence, inhibits their transportation. Such perturbations are likely to be a factor contributing to abnormal functioning of ion channels, resulting cell death and disease.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.08a
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• pp.150.2-150.2
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• 2013

We elucidate the mechanism of the self-assembled organic layer formation at the organic/metal interface of hexaaza-triphenylene-hexacarbonitrile (HATCN)/Au(111) by first-principles calculations and Lowtemperature scanning tunneling microscope (STM). In this work, we used HATCN to deposit organic material which is well known as an efficient OLED charge generation material. Low-temperature STM measurements revealed that self-assembled hexagonal porous structure is formed at terraces of Au(111). We also found that the hexagonal porous structure has chirality and forms only small (<1000 $nm^2$) phaseseparated chiral domains that can easily change their chiral phase in subsequence STM images at 80 K. To explain the mechanism of these observation, we calculated the molecular-molecular and molecule-surface interaction energies by using density functional theory method. We found that the change of their chiral phase resulted from the competition between the two energies. These results have not only verified our experimental observations, but also revealed the delicate balance between different interactions that caused the self-assembed structures at the surface.

• Membrane Journal
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• v.27 no.4
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• pp.358-366
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• 2017

The most important factor in the performances of polymer electrolyte membranes for fuel cells is how fast hydrogen ions can be transported along the water channel formed inside the electrolyte membrane. Since the morphology of the water channel and the diffusivity of the protons are very important factors for the proton transport behavior, various molecular dynamics simulation studies are being carried out to clarify this. The force-field is an important variable parameterizing the movement and interaction of each atom in molecular dynamics simulation. In this study, proton diffusivities of the 3D models of polymer electrolyte membranes were calculated in order to analyze the effects of various types of force-fields on the molecular simulation. It has been found that the charge value determining the non-bonding interaction plays a very important role in the formation of the water channel morphology, and the COMPASS force-field can calculate the accurate proton diffusion behavior. Accordingly, for molecular dynamics simulation of polymer electrolyte membranes, the proper selection of the force-field is very important due to its great effect on the proton diffusion as well as the final molecular structure.

• Journal of Microbiology and Biotechnology
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• v.30 no.8
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• pp.1261-1271
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• 2020

Cytochrome c_L (Cytc_L) is an essential protein in the process of methanol oxidation in methylotrophs. It receives an electron from the pyrroloquinoline quinone (PQQ) cofactor of methanol dehydrogenase (MDH) to produce formaldehyde. The direct electron transfer mechanism between Cytc_L and MDH remains unknown due to the lack of structural information. To help gain a better understanding of the mechanism, we determined the first crystal structure of heme c containing Cytc_L from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MP^T at 2.13 Å resolution. The crystal structure of Ma-Cytc_L revealed its unique features compared to those of the terrestrial homologues. Apart from Fe in heme, three additional metal ion binding sites for Na⁺, Ca⁺, and Fe²⁺ were found, wherein the ions mostly formed coordination bonds with the amino acid residues on the loop (G93-Y111) that interacts with heme. Therefore, these ions seemed to enhance the stability of heme insertion by increasing the loop's steadiness. The basic N-terminal end, together with helix α4 and loop (G126 to Y136), contributed positive charge to the region. In contrast, the acidic C-terminal end provided a negatively charged surface, yielding several electrostatic contact points with partner proteins for electron transfer. These exceptional features of Ma-Cytc_L, along with the structural information of MDH, led us to hypothesize the need for an adapter protein bridging MDH to Cytc_L within appropriate proximity for electron transfer. With this knowledge in mind, the methanol oxidation complex reconstitution in vitro could be utilized to produce metabolic intermediates at the industry level.

• Journal of the Korean Chemical Society
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• v.40 no.1
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• pp.11-19
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• 1996

The cationic polymerization of energetic substituted oxetanes which have pendant energetic group such as azido and nitrato are investigated theoretically, using semiempirical HF/3-21G, MINDO/3, MNDO and AM1 method. The stereo- and electronic structure of binary molecular complex composed of energetic substituted oxetane and boron trifluoride can be explain by molecular orbital theory. The reactivity of propagation in the copolymerization of oxetanes can be presented by the positive charge on carbon(C2) atom of oxetane and energy level of the lowest unoccupied molecular orbital(LUMO) of propagating species of oxetanes. The reactivity ratios for copolymerization of oxetanes are a random copolymer-zation which is agree with MO calculated and experimental results. The relative equlibrium concentration of cyclic oxonium and open carbenium ions is found to be a major determinant of mechanism, owing to the rapid equilibrium of these cation forms and the expectation based on calculation that in the prepolymer propagation step, SN1 mechanism will be at least as fast as that for SN2 mechanism.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.499-499
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• 2011

Silicon nanowires (Si NWs) have been extensively studied for nanoelectronics owing to their unique optical and electrical properties different from those of bulk silicon. For the development of Si NW devices, better understanding of oxidation behavior in Si NWs would be an important issue. For example, it is widely known that atomic scale roughness at the dielectric (SiOx)/channel (Si) interface can significantly affect the device performance in the nano-scale devices. However, the oxidation process at the atomic-scale is still unknown because of its complexity. In the present work, we investigated the oxidation behavior of Si NW in atomic scale by simulating the dry oxidation process using a reactive molecular dynamics simulation technique. We focused on the residual stress evolution during oxidation to understand the stress effect on oxidation behavior of Si NWs having two different diameters, 5 nm and 10 nm. We calculated the charge distribution according to the oxidation time for 5 and 10 nm Si NWs. Judging from this data, it was observed that the surface oxide layer started to form before it is fully oxidized, i.e., the active diffusion of oxygen in the surface oxide layer. However, it is well-known that the oxide layer formation on the Si NWs results in a compressive stress on the surface which may retard the oxygen diffusion. We focused on the stress evolution of Si NWs during the oxidation process. Since the surface oxidation results in the volume expansion of the outer shell, it shows a compressive stress along the oxide layer. Interestingly, the stress for the 10 nm Si NW exhibits larger compressive stress than that of 5 nm Si NW. The difference of stress level between 5 an 10 anm Si NWs is approximately 1 or 2 GPa. Consequently, the diameter of Si NWs could be a significant factor to determine the self-limiting oxidation behavior of Si NWs when the diameter was very small.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.31-32
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• 2010

In our previous reports [1-3], electron transport for the switching and memory devices using alkyl thiol-tethered Ru-terpyridine complex compounds with metal-insulator-metal crossbar structure has been presented. On the other hand, among organic memory devices, a memory based on the OFET is attractive because of its nondestructive readout and single transistor applications. Several attempts at nonvolatile organic memories involve electrets, which are chargeable dielectrics. However, these devices still do not sufficiently satisfy the criteria demanded in order to compete with other types of memory devices, and the electrets are generally limited to polymer materials. Until now, there is no report on nonvolatile organic electrets using nano-interfaced organic monomer layer as a dielectric material even though the use of organic monomer materials become important for the development of molecularly interfaced memory and logic elements. Furthermore, to increase a retention time for the nonvolatile organic memory device as well as to understand an intrinsic memory property, a molecular design of the organic materials is also getting important issue. In this presentation, we report on the OFET memory device built on a silicon wafer and based on films of pentacene and a SiO2 gate insulator that are separated by organic molecules which act as a gate dielectric. We proposed push-pull organic molecules (PPOM) containing triarylamine asan electron donating group (EDG), thiophene as a spacer, and malononitrile as an electron withdrawing group (EWG). The PPOM were designed to control charge transport by differences of the dihedral angles induced by a steric hindrance effect of side chainswithin the molecules. Therefore, we expect that these PPOM with potential energy barrier can save the charges which are transported to the nano-interface between the semiconductor and organic molecules used as the dielectrics. Finally, we also expect that the charges can be contributed to the memory capacity of the memory OFET device.[4]

• Polymer(Korea)
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• v.29 no.4
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• pp.363-367
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• 2005

The effects of organic solvent on the charge transport behavior of poly (3,4-ethylenedioxythioph one)/p-toluene-sulfonate(PEDOT-OTs) are investigated. The use of different organic solvents during the oxidative chemical polymerization of 3,4-ethylenedioxythiophene (EDOT) with Iron(III) -tosylate can greatly vary the DC conductivity of PEDOT-OTs along with molecular structure and doping concentration. For example, PEDOT-OTs prepared from methanol shows the conductivity of 19.5 S/cm, which is an increase by a factor of $10^8$ compared to PEDOT-OTa prepared from acetone. From the X-ray diffraction (XRD) experiments, it was found that PEDOT-OTs with ketone is amorphous state, while PEDOT-OTs with alcoholic solvent shows the better defined crystalline structure in which the charge transport along and between the PEDOT chains are promoted. Chemical analysis employing X-ray photoelectron spectroscopy (XPS) revealed that the doping concentration of PEDOT-OTs with alcoholic solvent is much higher than that of PEDOT-OTs with ketones. It is proposed that the interactions between the organic solvent and doping anion can cause the variation in doping concentration and, therefore, result in the PEDOT-OTs of different conductivities and chain structures.

• Journal of Surface Science and Engineering
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• v.42 no.1
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• pp.8-12
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• 2009

Electronic structures and chemical bonding of Li-intercalated $LiTiS_2$ and $LiTiO_2$ were investigated by using discrete variational $X{\alpha}$ method as a first-principles molecular-orbital method. ${\alpha}-NaFeO_2$ structure is the equilibrium structure for $LiCoO_2$, which is widely used as a commercial cathode material for lithium secondary battery. The study especially focused on the charge state of Li ions and the magnitude of covalency around Li ions. The average voltage of lithium intercalation was calculated using pseudopotential method and the average intercalation voltage of $LiTiO_2$ was higher than that of $LiTiS_2$. It can be explained by the differences in Mulliken charge of lithium and the bond overlap population between the intercalated Li ions and anions in $LiTiO_2$ as well as $LiTiS_2$. The Mulliken charge, which means the ionicity of Li atom, was approximately 0.12 in $LiTiS_2$ and the bond overlap population (BOP) indicating the covalency between Ti and S was about 0.339. One the other hands, the Mulliken charge of lithium was about 0.79, which means that Li is fully ionized. The BOP, the covalency between Ti and O, was 0.181 in $LiTiO_2$. Because of high ionicity of Li and the weak covalency between Ti and the nearest anion, $LiTiO_2$ has a higher intercalation voltage than that of $LiTiS_2$.

• Proceedings of the Ginseng society Conference
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• 1990.06a
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• pp.79-85
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• 1990

The aqueous extract of fresh ginseng (Panax ginseng C.A. Meyer) contains a macromolecular fraction that showed mitogenic and comitogenic activities in human peripheral blood Iymphocytes. Purification of the crude extract by size (ultrafiltration, Sephadex G-200) and charge (DEAE-cellulose. DEAE-Sepharose) yielded a semi-purified fraction (DS-3). This fraction contains at least three subgroups of anionic macromolecules with apparent molecular weight greater than 600 kilodaltons. It is a glycoprotein with a large amount of glucuronic acid. It acts as a mitogen in both T and B cells of human peripheral blood lymphocytes. It could also potentiate the mitogenic action of Concanavalin A in Iymphocyte T cells. Such potentiation is not due to increased binding of Concanavalin A to the cell surface. Its mitogenic and co-mitogenic effects do depend on the presence of extracellular Ca2+.