• Asian Journal of Atmospheric Environment
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• v.2 no.1
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• pp.34-46
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• 2008

Emissions inputs for use in air quality modeling of Korea were generated with the emissions inventory data from the National Institute of Environmental Research (NIER), maintained under the Clean Air Policy Support System (CAPSS) database. Source Classification Codes (SCC) in the Korea emissions inventory were adapted to use with the U.S. EPA's Sparse Matrix Operator Kernel Emissions (SMOKE) by finding the best-matching SMOKE default SCCs for the chemical speciation and temporal allocation. A set of 19 surrogate spatial allocation factors for South Korea were developed utilizing the Multi-scale Integrated Modeling System (MIMS) Spatial Allocator and Korean GIS databases. The mobile and area source emissions data, after temporal allocation, show typical sinusoidal diurnal variations with high peaks during daytime, while point source emissions show weak diurnal variations. The model-ready emissions are speciated for the carbon bond version 4 (CB-4) chemical mechanism. Volatile organic carbon (VOC) emissions from painting related industries in area source category significantly contribute to TOL (Toluene) and XYL (Xylene) emissions. ETH (Ethylene) emissions are largely contributed from point industrial incineration facilities and various mobile sources. On the other hand, a large portion of OLE (Olefin) emissions are speciated from mobile sources in addition to those contributed by the polypropylene industry in point source. It was found that FORM (Formaldehyde) is mostly emitted from petroleum industry and heavy duty diesel vehicles. Chemical speciation of PM2.5 emissions shows that PEC (primary fine elemental carbon) and POA (primary fine organic aerosol) are the most abundant species from diesel and gasoline vehicles. To reduce uncertainties in processing the Korea emission inventory due to the mapping of Korean SCCs to those of U.S., it would be practical to develop and use domestic source profiles for the top 10 SCCs for area and point sources and top 5 SCCs for on-road mobile sources when VOC emissions from the sources are more than 90% of the total.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.75-75
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• 2003

We report here the results on N-acetyl-N'-dimethylamide of proline (Ac-Pro-NM $e_2$) calculated using the ab initio molecular orbital method with the self-consistent reaction field (SCRF) theory at the HF level with the 6-31+G(d) basis set to investigate the conformational preference of polyproline depending on the cis/trans peptide bonds and down/up puckerings along the backbone torsion angle $\square$ in the gas phase, chloroform, and water. In the gas phase, Ac-Pro-NM $e_2$ has seven local minima of tFd, tFu, cFd, cFu, cAu, tAu, and cAd conformations. In particular, polyproline conformations tFd, tFu, cFd, and cFu are found to be more stable than $\square$-helical conformations cAu, tAu, and cAd. In contrast, Ac-Pro-NHMe has seven local minima of tCd, tCu, cBd, cAu, tAu, cFd, and cFu conformations. Conformations tCd and tCu are found to be most stable, which is ascribed to the intramolecular hydrogen bond between C=O of acetyl group and $N^{~}$ H of N'-methyl amide group. The stability of the cFd conformation (i.e., the polyproline I structure) in chloroform is somewhat increased, relative to that in water, although tFd and tFu conformations (i.e., the polyproline II structure) are dominate both in chloroform and water. The population of backbone conformations feasible in chloroform and water is consistent with the experiments. This work is supported by a Korea Research Foundation Grant (KRF-2002-041-C00129).

• Archives of Pharmacal Research
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• v.29 no.1
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• pp.50-58
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• 2006

Translationally controlled tumor protein (TCTP), also known as histamine releasing factor (HRF), is found abundantly in different eukaryotic cell types. The sequence homology of TCTP between different species is very high, belonging to the MSS4/DSS4 superfamily of proteins. TCTP is involved in both cell growth and human late allergy reaction, as well as having a calcium binding property; however, its primary biological functions remain to be clearly elucidated. In regard to many possible functions, the TCTP of Plasmodium falciparum (Pf) is known to bind with an antimalarial agent, artemisinin, which is activated by heme. It is assumed that the endoperoxide-bridge of artemisinin is opened up by heme to form a free radical, which then eventually alkylates, probably to the Cys14 of PfTCTP. Study of the docking of artemisinin with heme, and subsequently with PfTCTP, was carried out to verify the above hypothesis on the basis of structural interactions. The three dimensional (3D) structure of PfTCTP was built by homology modeling, using the NMR structure of the TCTP of Schizosaccharomyces pombe as a template. The quality of the model was examined based on its secondary structure and biological function, as well as with the use of structure evaluating programs. The interactions between artemisinin, heme and PfTCTP were then studied using the docking program, FlexiDock. The center of the peroxide bond of artemisinin and the Fe of heme were docked within a short distance of $2.6{\AA}$, implying the strong possibility of an interaction between the two molecules, as proposed. When the activated form of artemisinin was docked on the PfTCTP, the C4-radical of the drug faced towards the sulfur of Cys14 within a distance of $2.48{\AA}$, again suggesting the possibility of alkylation having occurred. These results confirm the proposed mechanism of the antimalarial effect of artemisinin, which will provide a reliable method for establishing the mechanism of its biological activity using a molecular modeling study.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1704-1710
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• 2010

The structure of a 2D grid-like copper(II) complex [Cu$(NCO)_2$(pyz)](pyz=pyrazine) (1) consists of 1D chains of Cu-pyz units connected by double end-on (EO) cyanato bridges. Each Cu(II) ion has a distorted octahedral coordination, completed by the four EO cyanato and two pyrazine ligands. Magnetic interactions through EO cyanato and pyrazine bridges in 1 are discussed on the basis of DFT broken-symmetry calculations at the B3LYP level. For model dicopper(II) complexes I (bridged by cyanato) and II (bridged by pyrazine), electronic structure calculations reproduce very well the experimental couplings for the S = 1/2 ferromagnetic and antiferromagnetic exchange-coupled 2D system: the calculated exchange parameters J are +1.25 $cm^{-1}$ and -3.07 $cm^{-1}$ for I and II, respectively. The $\sigma$ orbital interactions between the Cu $x^2-y^2$ magnetic orbitals and the nitrogen lone-pair orbitals of pyrazine are analyzed from the viewpoint of through-bond interaction. The energy splitting of 0.106 eV between two SOMOs indicates that the superexchange interaction should be antiferromagnetic in II. On the other hand, there are no bridging orbitals that efficiently connect the two copper(II) magnetic orbitals in I because the HOMOs of the basal-apical NCO bridge do not play a role in the formation of overlap interaction pathway. The energy separation in the pair of SOMOs of I is calculated to be very small (0.054 eV). This result is consistent with the occurrence of weakly ferromagnetic properties in I.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.27 no.2
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• pp.87-94
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• 2014

In solid mechanics, the peridynamics theory has provided a suitable framework for material failure and damage propagation simulation. Peridynamics is computationally expensive since it is required to solve enormous nonlocal interactions based upon integro-differential equations. Thus, multiscale coupling methods with other local models are of interest for efficient and accurate implementations of peridynamics. In this study, peridynamic models are restricted to regions where discontinuities or stress concentrations are present. In the domains characterized by smooth displacements, classical local models can be employed. We introduce a recently developed blending scheme to concurrently couple bond-based peridynamic models and the Navier equation of classical elasticity. We demonstrate numerically that the proposed blended model is suitable for point loads and static fracture, suggesting an alternative framework for cases where peridynamic models are too expensive, while classical local models are not accurate enough.

• Smart Structures and Systems
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• v.17 no.2
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• pp.297-311
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• 2016

Based on the distributed fiber optic sensing (DFOS) technique, plastic optical fibers (POFs) are attractive candidates to measure deformations of geotechnical structures because they can withstand large strains before rupture. Understanding the mechanical interaction between an embedded POF and the surrounding soil or rock is a necessary step towards establishing an effective POF-based sensing system for geotechnical monitoring. This paper describes a first attempt to evaluate the feasibility of POF-based soil deformation monitoring considering the POF-soil interfacial properties. A series of pullout tests were performed under various confining pressures (CPs) on a jacketed polymethyl methacrylate (PMMA) POF embedded in soil specimens. The test results were interpreted using a fiber-soil interaction model, and were compared with previous test data of silica optical fibers (SOFs). The results showed that the range of CP in this study did not induce plastic deformation of the POF; therefore, the POF-soil and the SOF-soil interfaces had similar behavior. CP was found to play an important role in controlling the fiber-soil interfacial bond and the fiber measurement range. Moreover, an expression was formulated to determine whether a POF would undergo plastic deformation when measuring soil deformation. The plasticity of POF may influence the reliability of measurements, especially for monitored geo-structures whose deformation would alternately increase and decrease. Taken together, these results indicate that in terms of the interfacial parameters studied here the POF is feasible for monitoring soil deformation as long as the plastic deformation issue is carefully addressed.

• Structural Engineering and Mechanics
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• v.75 no.6
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• pp.643-657
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• 2020

This study presents experimental and numerical investigations on circular steel tube confined ultra high performance concrete (UHPC) columns under axial compression. The plain UHPC without fibers was designed to achieve a compressive strength ranged between 150 MPa and 200 MPa. Test results revealed that loading on only the UHPC core can generate a significant confinement effect for the UHPC core, thus leading to an increase in both strength and ductility of columns, and restricting the inherent brittleness of unconfined UHPC. All tested columns failed by shear plane failure of the UHPC core, this causes a softening stage in the axial load versus axial strain curves. In addition, an increase in the steel tube thickness or the confinement index was found to increase the strength and ductility enhancement and to reduce the magnitude of the loss of load capacity. Besides, steel tube with higher yield strength can improve the post-peak behavior. Based on the test results, the load contribution of the steel tube and the concrete core to the total load was examined. It was found that no significant confinement effect can be developed before the peak load, while the ductility of post-peak stage is mainly affected by the degree of the confinement effect. A finite element model (FEM) was also constructed in ABAQUS software to validate the test results. The effect of bond strength between the steel tube and the UHPC core was also investigated through the change of friction coefficient in FEM. Furthermore, the mechanism of circular steel tube confined UHPC columns was examined using the established FEM. Based on the results of FEM, the confining pressures along the height of each modeled column were shown. Furthermore, the interaction between the steel tube and the UHPC core was displayed through the slip length and shear stresses between two surfaces of two materials.

• Journal of the Institute of Electronics Engineers of Korea SD
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• v.41 no.8
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• pp.1-8
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• 2004

Experimental results are presented for gate oxide degradation, such as SILC and soft breakdown, and its effect on device parameters under negative and positive bias stress conditions using n-MOSFET's with 3 nm gate oxide. The degradation mechanisms are highly dependent on stress conditions. For negative gate voltage, both interface and oxide bulk traps are found to dominate the reliability of gate oxide. However, for positive gate voltage, the degradation becomes dominated mainly by interface trap. It was also found the trap generation in the gate oxide film is related to the breakage of Si-H bonds through the deuterium anneal and additional hydrogen anneal experiments. Statistical parameter variations as well as the “OFF” leakage current depend on both electron- and hole-trapping. Our results therefore show that Si or O bond breakage by tunneling electron and hole can be another origin of the investigated gate oxide degradation. This plausible physical explanation is based on both Anode-Hole Injection and Hydrogen-Released model.

• Molecules and Cells
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• v.37 no.4
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• pp.322-329
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• 2014

N-acetylglucosamine kinase (GlcNAc kinase or NAGK; EC 2.7.1.59) is highly expressed and plays a critical role in the development of dendrites in brain neurons. In this study, the authors conducted structure-function analysis to verify the previously proposed 3D model structure of GlcNAc/ATP-bound NAGK. Three point NAGK mutants with different substrate binding capacities and reaction velocities were produced. Wild-type (WT) NAGK showed strong substrate preference for GlcNAc. Conversion of Cys143, which does not make direct hydrogen bonds with GlcNAc, to Ser (i.e., C143S) had the least affect on the enzymatic activity of NAGK. Conversion of Asn36, which plays a role in domain closure by making a hydrogen bond with GlcNAc, to Ala (i.e., N36A) mildly reduced NAGK enzyme activity. Conversion of Asp107, which makes hydrogen bonds with GlcNAc and would act as a proton acceptor during nucleophilic attack on the ${\gamma}$-phosphate of ATP, to Ala (i.e., D107A), caused a total loss in enzyme activity. The overexpression of EGFP-tagged WT or any of the mutant NAGKs in rat hippocampal neurons (DIV 5-9) increased dendritic architectural complexity. Finally, the overexpression of the small, but not of the large, domain of NAGK resulted in dendrite degeneration. Our data show the effect of structure on the functional aspects of NAGK, and in particular, that the small domain of NAGK, and not its NAGK kinase activity, plays a critical role in the upregulation of dendritogenesis.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.4-5
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• 2010

The surface phonon is defined as a coherent vibrational excitation of surface atoms propagating along the surface. It is characterized by a phonon dispersion curves, which were extensively studied in 1990's using helium atom scattering and high-resolution electron-energy-loss spectroscopy (HREELS)[1].The understanding is mainly based on the theoretical framework of a classical bond model or cluster calculations. The recent sample preparation and first principles calculations open the naval way to deep insight for surface phonon problems. The surface phonon dispersion on the hydrogen-terminated Si(111)-($1{\times}1$) surface [H:Si(111)] is the typical system and already reported experimentally [2] and theoretically [3], although the understandingis incomplete. The sample contaminated by the oxygen atoms on the surface and the calculations were also classical. In this study, firstly, we have prepared an ultra-clean H:Si(111) surface [4] and measured the surface phonon dispersion curvesusing HREELS. Secondly, we have performed first-principles density functional calculations with the projector augmented wave functionals, as implemented in VASP, using generalized gradient approximations. We used aslab of six silicon layers and both top and bottom surfaces were terminated with hydrogen atoms. Finally, we have compared with the surface phonon dispersion of deuterium-terminatedSi(111)-($1{\times}1$) surface[5] and led to our conclusions. The Si-H stretching and the bending modes are observed at 258.5 and 78.2 meV, respectively. These energies are the same as the previously reported values [2], but the energy-loss peaks at the lower energy regions are dramatically shifted. Through this combination study, we have formulated the procedure of preparing ultra-clean H:Si(111)/D:Si(111), which was confirmed by HREELS vibrational analysis. The Si surface will be utilized for further nano-physics research as well as for the materials for nano-fubrication.