• Proceedings of the Korean Vacuum Society Conference
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• 2010.08a
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• pp.32-32
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• 2010

Since the characteristics of plasmas depend strongly on the interactions between plasma particles such as electron, ions, and neutrals, a well-established atomic and molecular database is needed to understand and produce various types of plasma. Thus, National Fusion Research Institute (NFRI) started to establish the plasma property DB for fusion and industrial plasma from last 2002. Here we describe our recent data evaluation activities regarding to production of atomic and molecular data that are needed for modeling plasma in fusion tokamaks and also low temperature industrial plasmas.

• Proceedings of the Korean Vacuum Society Conference
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• 2015.08a
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• pp.64-64
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• 2015

Control of plasma processing methodologies can only occur by obtaining a thorough understanding of the physical and chemical properties of plasmas. However, all plasma processes are currently used in the industry with an incomplete understanding of the coupled chemical and physical properties of the plasma involved. Thus, they are often 'non-predictive' and hence it is not possible to alter the manufacturing process without the risk of considerable product loss. Only a more comprehensive understanding of such processes will allow models of such plasmas to be constructed that in turn can be used to design the next generation of plasma reactors. Developing such models and gaining a detailed understanding of the physical and chemical mechanisms within plasma systems is intricately linked to our knowledge of the key interactions within the plasma and thus the status of the database for characterizing electron, ion and photon interactions with those atomic and molecular species within the plasma and knowledge of both the cross-sections and reaction rates for such collisions, both in the gaseous phase and on the surfaces of the plasma reactor. The compilation of databases required for understanding most plasmas remains inadequate. The spectroscopic database required for monitoring both technological and fusion plasmas and thence deriving fundamental quantities such as chemical composition, neutral, electron and ion temperatures is incomplete with several gaps in our knowledge of many molecular spectra, particularly for radicals and excited (vibrational and electronic) species. However, the compilation of fundamental atomic and molecular data required for such plasma databases is rarely a coherent, planned research program, instead it is a parasitic process. The plasma community is a rapacious user of atomic and molecular data but is increasingly faced with a deficit of data necessary to both interpret observations and build models that can be used to develop the next-generation plasma tools that will continue the scientific and technological progress of the late 20th and early 21st century. It is therefore necessary to both compile and curate the A&M data we do have and thence identify missing data needed by the plasma community (and other user communities). Such data may then be acquired using a mixture of benchmarking experiments and theoretical formalisms. However, equally important is the need for the scientific/technological community to recognize the need to support the value of such databases and the underlying fundamental A&M that populates them. This must be conveyed to funders who are currently attracted to more apparent high-profile projects.

• Analytical Science and Technology
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• v.8 no.4
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• pp.443-448
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• 1995

Three anode configurations of six-jet, cone-jet and cylindrical-jet are tested for their analytical performance under power mode operation. The effect of pressure, power and gas flow rate on atomic absorption signals have been studied. The increase of atomic absorption signal of sample element is observed at a fixed pressure in all configurations as the gas flow rate increase up to 300-600 seem, and as the power dissipated in the glow discharge cell increase. The lower the pressure is in the glow discharge cell at a fixed discharge power and argon flow rate, the greater the absorbance of sample element is. The optimum conditions are taken from these data and a calibration curve of Cu in low-alloy steel sample is obtained. In this calibration curve, six-jet configuration shows the best analytical results varies as the sample element.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.268-274
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• 2003

Most currently known molecular structures were determined by X-ray crystallography or Nuclear Magnetic Resonance (NMR). These methods generate a large amount of structure data, even far small molecules, and consist mainly of three-dimensional atomic coordinates. These are useful for analyzing molecular structure, but structure elements at higher level are also needed for a complete understanding of structure, and especially for structure prediction. Computational approaches exist for identifying secondary structural elements in proteins from atomic coordinates. However, similar methods have not been developed for RNA due in part to the very small amount of structure data so far available, and extracting the structural elements of RNA requires substantial manual work. Since the number of three-dimensional RNA structures is increasing, a more systematic and automated method is needed. We have developed a set of algorithms for recognizing secondary and tertiary structural elements in RNA molecules and in the protein-RNA structures in protein data banks (PDB). The present work represents the first attempt at extracting RNA structure elements from atomic coordinates in structure databases. The regularities in the structure elements revealed by the algorithms should provide useful information for predicting the structure of RNA molecules bound to proteins.

• Bulletin of the Korean Chemical Society
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• v.25 no.7
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• pp.1061-1064
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• 2004

Molecular visualization software has the common objective of manipulation and interpretation of data from numerical simulations. They visualize many complicated molecular structures with personal computer and workstation, to help analyze a large quantity of data produced by various computational methods. However, users are often discouraged from using these tools for visualization and analysis due to the difficult and complicated user interface. In this regard, we have developed an easy-to-use three-dimensional molecular visualization and analysis program named POSMOL. This has been developed on the Microsoft Windows platform for the easy and convenient user environment, as a compact program which reads outputs from various computational chemistry software without editing or changing data. The program animates vibration modes which are needed for locating minima and transition states in computational chemistry, draws two and three dimensional (2D and 3D) views of molecular orbitals (including their atomic orbital components and these partial sums) together with molecular systems, measures various geometrical parameters, and edits molecules and molecular structures.

• Bulletin of the Korean Chemical Society
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• v.30 no.4
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• pp.857-862
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• 2009

We model lattice-mismatched group III-V semiconductor $In_{x}Ga_{1-x}$ alloys with the three-parameter anharmonic Kirkwood-Keating potential, which includes realistic distortion effect by introducing anharmonicity. Although the potential parameters were determined based on optical properties of the binary parent alloys InAs and GaAs, simulated dielectric functions, reflectance, and Raman spectra of alloys agree excellently with experimental data for any arbitrary atomic composition. For a wide range of atomic composition, InAs- and GaAs-bond retain their respective properties of binary parent crystals despite lattice and charge mismatch. It implies that use of the anharmonic Kirkwood-Keating potential may provide an optimal model system to investigate diverse and unique optical properties of quantum dot heterostructures by circumventing potential parameter searches for particular local structures.

• Nuclear Engineering and Technology
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• v.36 no.5
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• pp.375-387
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• 2004

This paper presents a transient multicomponent mixture analysis tool developed to analyze the molecular diffusion, natural convection, and chemical reactions related to air ingress phenomena that occur during a primary-pipe rupture of a high temperature gas-cooled reactor (HIGR). The present analysis tool solves the one-dimensional basic equations for continuity, momentum, energy of the gas mixture, and the mass of each gas species. In order to obtain numerically stable and fast computations, the implicit continuous Eulerian scheme is adopted to solve the governing equations in a strongly coupled manner. Two types of benchmark calculations were performed with the data of prerious Japanese inverse U-tube experiments. The analysis program, based on the ICE technique, runs about 36 times faster than the FLUENT6 for the simulation of the two experiments. The calculation results are within a 10% deviation from the experimental data regarding the concentrations of the gas species and the onset times of natural convection.

• BMB Reports
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• v.31 no.6
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• pp.525-535
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• 1998

A critical step in the faithful translation of genetic information is specific tRNA recognition by aminoacyl-tRNA synthetases. These enzymes catalyze the covalent attachment of particular amino acids to the terminal adenosine of cognate tRNA substrates. In general, there is one synthetase for each of the twenty amino acids and each enzyme must discriminate against all of the cellular tRNAs that are specific for the nineteen noncognate amino acids. Primary sequence information combined with structural data have resulted in the division of the twenty synthetases into two classes. In recent years, several high-resolution co-crystal structures along with biochemical data have led to an increased understanding of tRNA recognition by synthetases of both classes. The anticodon sequence and the amino acid acceptor stem are the most common locations for critical recognition elements. This review will focus on acceptor stem discrimination by class II synthetases. In particular, the results of in vitro aminoacylation assays and site-directed and atomic group mutagenesis studies will be discussed. These studies have revealed that even subtle atomic determinants can provide signals for specific tRNA aminoacylation.

• Journal of The Korean Astronomical Society
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• v.32 no.1
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• pp.41-53
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• 1999

We have carried out high-resolution observations along one-dimensional cuts through the three Galactic super-shells GS 064-01-97, GS 090-28-17, and GS 174+02-64 in the HI 21 cm and CO J=l-0 lines. By comparing the HI data with IRAS data, we have derived the distributions of the $I_{100}$ and $T_{100}$ excesses, which are, respectively, the 100 ${\mu}m$ intensity and 100 ${\mu}m$ optical depth in excess of what would be expected from HI emission. We have found that both the $I_{100}$ and $T_{100}$ excesses have good correlations with the CO integrated intensity W co in all three supershells. But the $I_{100}$ excess appears to underestimate $H_2$ column density N($H_2$) by factors of 1.5-3.8. This factor is the ratio of atomic to molecular infrared emissivities, and we show that it can be roughly determined from the HI and IRAS data. By comparing the $T_{100}$ excess with $W_{co}$, we derive the conversion factor X $\equiv$ N ($H_2$) /$W_{co}{\simeq}$ 0.26 - 0.66 in the three supershells. In GS 090- 28-17, which is a very diffuse shell, our result suggests that the region with N($H_2$) $\le$ $3 {\times} 10^{20} cm^{-2}$ does not have observable CO emission, which appears to be consistent with previous results indicating that diffuse molecular gas is not observable in CO. Our results show that the molecular gas has a 60/100 ${\mu}m$ color temperature $T_d$ lower than the atomic gas. The low value of $T_d$ might be due either to the low equilibrium temperature or to the lower abundance of small grains, or a combination of both.

• Mass Spectrometry Letters
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• v.11 no.3
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• pp.41-51
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• 2020

Microbes influence many aspects of human life from the environment to health, yet evaluating their biological processes at the chemical level can be problematic. Mass spectrometry imaging (MSI) enables direct evaluation of microbial chemical processes at the atomic to molecular levels without destruction of valuable two-dimensional information. MSI is a label-free method that allows multiplex spatiotemporal visualization of atomic- or molecular-level information of microbial and microberelated samples. As a result, microbial MSI has become an important field for both mass spectrometrists and microbiologists. In this review, basic techniques for microbial MSI, such as ionization methods and analyzers, are explored. In addition, we discuss practical applications of microbial MSI and various data-processing techniques.