• Genomics & Informatics
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• v.6 no.2
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• pp.72-76
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• 2008

Hypoxia-inducible factor $1{\alpha}\;(HIF1{\alpha})$ is a transcription factor that plays a key role in the adaptation of cells to low oxygen stress and oxygen homeostasis. The oxygen-dependent degradation (ODD) domain of $HIF1{\alpha}$ is responsible for the negative regulation of $HIF1{\alpha}$ in normoxia. The interactions of the $HIF1{\alpha}$ ODD domain with partner proteins such as von Hippel-Lindau tumor suppressor (pVHL) and p53 are mediated by two sequence motifs, the N- and C-terminal ODD(NODD and CODD). Multiple sequence alignment with $HIF1{\alpha}$ homologs from human, monkey, pig, rat, mouse, chicken, frog, and zebrafish has demonstrated that the NODD and CODD motifs have noticeably high conservation of the primary sequence across different species and isoforms. In this study, we carried out molecular dynamics simulation of the structure of the $HIF1{\alpha}$ CODD motif in complex with the p53 DNA-binding domain (DBD). The structure reveals specific functional roles of highly conserved residues in the CODD sequence motif of $HIF1{\alpha}$ for the recognition of p53.

• Economic and Environmental Geology
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• v.32 no.1
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• pp.101-111
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• 1999

Sedimentary organic matter, exposed to continental surficial environment, reacts with oxygen supplied from the atmosphee and forms carbon-containing oxidation products. Knowledge of the rate and mechanisms of sedimentary organic matter weathering is important because it is one of the major controls on atmospheric oxygen level through geologic time. Under the abiological conditions, the oxidation rate of coal organic matter by molecular oxygen is enhanced by the increase of oxygen concentration and temperature. At ambient temperature and pressure, aqueous coal oxidation results in the formation of dissolved $CO_2$ dissolved organic carbon and solid oxidation products which are all quantitatively significant reaction products. The effects of pH, ultraviolet light, and microbial activity on the weathering of sedimentary organic matter are poorly contrained. Based on the results of geochmical and environmental studies, it is believed that the photochemical reaction should play an important role in the decomposition and oxidation of sedimentary organic matter removed from the weathering profile. At higher pH conditions, the production rate of DOC can be accelerated due to base catalysis. These high molecular weight oranic matter can react with man-made pollutants such as heavy metal ions via adsorption/desorption or ion exchange reactions. The effect of microbial activity on the oxidative weathering of sedimentary organic matter is poorly understood and remains to be studied.

• Membrane Journal
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• v.7 no.1
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• pp.15-21
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• 1997

Carbon molecular sieve (CMS) membranes were synthesized by the pyrolysis of polymeric precursors. The CMS materials had oxygen-nitrogen selectivities much higher than those observed for the polymeric precursors. Typically molecular sieving materials have diffusion selectivities much higher than polymeric materials. This has been identified as a result of higher entropic selectivity of the molecular sieving materials. A study of the development of molecular sieving properties as the polymeric precursor is pyrolyzed into a CMS material will offer us an insight into polymeric molecular structures needed for enhanced entropic selectivity membrane materials.

• Journal of Hydrogen and New Energy
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• v.11 no.4
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• pp.179-188
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• 2000

The anodic reaction of hydrogen/oxygen gas mixture at platinum or palladium electrode interfacing with a solid polymer electrolyte was investigated using AC impedance method. The impedance spectrum of the electrode reactions of the mixture depends on the gas composition, electrode roughness, the mode of electrochemical operation and the cell potential. For electrolysis mode of operation, the spectrum taken for the reaction on a rough platinum electrode for the gas mixture revealed clearly that the local anodic reduction of oxygen gas takes place concurrently with the anodic oxidation of hydrogen gas.

• Journal of the Korean Ceramic Society
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• v.44 no.3 s.298
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• pp.175-181
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• 2007

Molecular dynamics simulation (MD) of $(62-x)CaO{\cdot}38Al_{2}O_{3}{\cdot}xBaO$ glasses has been carried out using empirical potentials with the covalent term. The simulations closely reproduce the total neutron correlation functions of glass with 5 mol% BaO and physical properties of these glasses such as elastic constants. For these glasses, aluminum is tetrahedrally coordinated by oxygen, but there is a part of five-fold and six-fold coordination of aluminum. There are no major changes to the mid-range structure of glass, as barium is substituted for calcium. To predict the barium coordination number, we have used the bond valence (BV) theory and also compared the results of simulation with Bond valence. The coordination number for oxygen around barium atoms is close to 8 and the average distance of barium and oxygen is nearly 2.80 A. The viscosity of these glasses increases with the content of barium oxide substituted for calcium oxide.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.325-325
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• 2011

Very initial stage of oxidation process of Si (001) surface at room temperature (300 K) and high temperature (1200 K) was investigated using large scale molecular dynamics simulation. Reactive force field potential [1] was used for the simulation owing to its ability to handle charge variation as well as breaking and forming of bonds associated with the oxidation reaction. The results show that oxygen molecules adsorb dissociatively or otherwise leave the silicon surface. Initial position and orientation of oxygen molecule above the surface play important role in determining final state and time needed to dissociate. At 300 K, continuous transformation of ion $Si^+$ (or suboxide Si2O) to $Si2^+$ (SiO), $Si3^+$ (Si2O3) and finally to $Si4^+$ (SiO2) clearly observed. High temperature silicon surface provide heat energy that enable oxygen atom to penetrate into deeper silicon surface. The heat energy also retards adsorption process. As a result, transformation of ion $Si^+$ is impeded at 1200 K.

• Molecules and Cells
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• v.37 no.9
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• pp.637-643
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• 2014

Wound healing is a complex multi-step process that requires spatial and temporal orchestration of cellular and non-cellular components. Hypoxia is one of the prominent microenvironmental factors in tissue injury and wound healing. Hypoxic responses, mainly mediated by a master transcription factor of oxygen homeostasis, hypoxia-inducible factor-1 (HIF-1), have been shown to be critically involved in virtually all processes of wound healing and remodeling. Yet, mechanisms underlying hypoxic regulation of wound healing are still poorly understood. Better understanding of how the wound healing process is regulated by the hypoxic microenvironment and HIF-1 signaling pathway will provide insight into the development of a novel therapeutic strategy for impaired wound healing conditions such as diabetic wound and fibrosis. In this review, we will discuss recent studies illuminating the roles of HIF-1 in physiologic and pathologic wound repair and further, the therapeutic potentials of HIF-1 stabilization or inhibition.

• Journal of Korea Technical Association of The Pulp and Paper Industry
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• v.36 no.1
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• pp.37-42
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• 2004

ECF and TCF bleaching methods are favored in bleaching plants over the world due to the increasing environment constraints. However, interaction of main stages(D and O stage) in ECF bleaching have not been understood completely yet. The degradation of holocellulose as a carbohydrate model compound was investigated by SEC(size exclusive chromatography) to estimate the change of its molecular weight distribution after O and D stage combination treatment. The molecular weight distribution of holocellulose was observed in two divisions(higher and lower molecular portions). It was also shown that DO sequence was more effective than OD, and DOD or ODO was more effective than DO. D stage had a little effect on the degradation of holocellulose, while the degradation of holocellulose increased as the time of the first O stage increased.

• Journal of the Korean Crystal Growth and Crystal Technology
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• v.9 no.4
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• pp.381-383
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• 1999

First topic of this paper aims to clarify how oxygen and heat transfer in silicon melt under cusp-shaped magnetic fields. We obtained asymmetric temperature distribution by using time dependent and three-dimensional calculation. Second topic is study on molecular dynamics simulation, which was carried out to estimate diffusion constants of oxygen in silicon melt.

• Membrane Journal
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• v.33 no.6
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• pp.447-453
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• 2023

The performance of computer systems and the development of various computer simulation programs have made it possible to analyze chemical systems composed of more complex elements, and accordingly, research using molecular dynamics simulation is being actively conducted. Research on calculating the gas permeation characteristics of polymer membranes by molecular dynamics, which was previously conducted mainly through experiments, is receiving attention for gas barrier membranes used in food packaging and pharmaceuticals. Recently, there has been a report that a gas barrier effect appears when a coating film is made using silk fibroin, and in this study, a study was conducted using molecular dynamics simulation to confirm whether an oxygen barrier effect appears when a composite film is made using silk fibroin. We built a single model, calculated the gas permeation characteristics, and compared it with the experimental value to confirm that the model reflects the actual experimental results. Actual composite membrane models were then built and the gas movement path within the polymer was analyzed. As a result, oxygen molecules were found that they could not pass through and was blocked in the fibroin region. Therefore, the composite membrane with silk fibroin has excellent oxygen barrier property and is expected to be useful in food packaging, etc.