• Journal of Mechanical Science and Technology
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• v.18 no.12
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• pp.2104-2113
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• 2004

Surface degreasing method with premixed flame is proposed as the removal method of adherent impurities on materials. Effects of adherent molecular thickness and surface potential energy on evaporation rate of adherent molecules and molecular evaporation mechanism were investigated and discussed in the present study. Evaporation processes of adherent molecules on surface molecules were simulated by the molecular dynamics method to understand thermal phenomena on evaporation processes of adherent molecules by using high temperature gas like burnt gas. The calculation system was composed of a high temperature gas region, an adherent molecular region and a surface molecular region. Both the thickness of adherent molecules and potential parameters affceted the evaporation rate of adherent molecules and evaporation mechanism in molecular scale.

• BMB Reports
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• v.37 no.2
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• pp.148-152
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• 2004

A new molecular-baiting method was studied by retrieving targeted gene fragments from an oligonucleotide microarray bait after hybridization. To make the microarray bait, 70-mer oligonucleotides that were designed to specifically represent the SSA1 gene of Saccharomyces cerevisiae were printed on the slide. Samples of the Saccharomyces cerevisiae mRNA were extracted and labeled by the RD-PCR (Restriction Display PCR) method using the Cy5-labelled universal primer, then applied for hybridization. The sample fragments that hybridized to the microarray were stripped, and the eluted cDNAs were retrieved and cloned into the pMD 18-T vector for transformation, plasmid preparation, and sequencing. BLAST searching of the GenBank database identified the retrieved fragments as being identical to the SSA1 gene (from 2057-2541bp). A new method is being established that can retrieve the sample fragments using an oligo-microarray-bait.

• Journal of Advanced Marine Engineering and Technology
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• v.31 no.8
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• pp.932-938
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• 2007

The interaction between adherent molecules and gas molecules was modeled in molecular scale and simulated by the molecular dynamics method in order to understand the evaporation and removal processes of adherent molecules on metallic surface using high temperature gas flow. Methanol molecules were chosen as adherent molecules to investigate effects of adhesion quantify and gas molecular collisions because the industrial oil has too complex structures of fatty acid. The effects of adherent quantify, gas temperature and surface temperature for the evaporation rate of adherent molecules and the molecular removal mechanism were investigated and discussed in the present study. Evaporation and removal rates of adherent molecules from metallic surface calculated by the molecular dynamics method showed the similar dependence on surface temperature shown in the experimental results.

• International Journal of Automotive Technology
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• v.7 no.2
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• pp.121-128
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• 2006

The interaction between adherent molecules and gas molecules was modeled in the molecular scale and simulated by the molecular dynamics method in order to understand evaporation and removal processes of adherent molecules on metallic surface using high temperature gas flow. Methanol molecules were chosen as adherent molecules to investigate effects of adhesion quantity and gas molecular collisions because the industrial oil has too complex structures of fatty acid. Effects of adherent quantity, gas temperature, surface temperature and adhesion strength for the evaporation rate of adherent molecules and the molecular removal mechanism were investigated and discussed in the present study. Evaporation and removal rates of adherent molecules from metallic surface calculated by the molecular dynamics method showed the similar dependence on the surface temperature shown in the experimental results.

• BMB Reports
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• v.37 no.3
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• pp.356-361
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• 2004

To develop a simplified method that can rapidly prepare DNA microarray probes in a massive scale, a lambda phage genomic DNA-fragments library was constructed for the microarray-probes collection. Four methods of DNA band recovery from the first PCR products were tested and compared. The DNA microarray probes were collected by a novel method of nested PCR that was mediated by gel isolation of the first PCR products. This method was named GIN-PCR. The probes that were prepared by this GIN-PCR technique were used as subjects to fabricate a DNA microarray. The results showed that a wooden toothpick was superior to the other 3 methods, since this technique can steadily transfer the DNA bands as the template of the second PCR after the first PCR. A group of probes were successfully collected and DNA microarrays were constructed using these probes. Hybridization results demonstrated that this technique of DNA recovery and probe preparation was rapid, efficient, and effective. We developed a cost-effective and less labor-intensive method for DNA microarray probe preparation by nested PCR that is mediated by wooden toothpick transfer of the DNA bands in the gel after electrophoresis.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.797-801
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• 2003

One of the largest challenges for quantum chemistry today is to obtain accurate results for large complex molecular systems, and a variety of approaches have been proposed recently toward this goal. We have developed the ONIOM method, an onion skin-like multi-level method, combining different levels of quantum chemical methods as well as molecular mechanics method. We have been applying the method to many different large systems, including thermochemistry, homogeneous catalysis, stereoselectivity in organic synthesis, solution chemistry, fullerenes and nanochemistry, and biomolecular systems. The method has recently been combined with the polarizable continuum model (ONIOM-PCM), and was also extended for molecular dynamics simulation of solution (ONIOM-XS). In the present article the recent progress in various applications of ONIOM and other electronic structure methods to problems of homogeneous catalyses and nanochemistry is reviewed. Topics include 1. bond energies in large molecular systems, 2. organometallic reactions and homogeneous catalysis, 3. structure, reactivity and bond energies of large organic molecules including fullerenes and nanotubes, and 4. biomolecular structure and enzymatic reaction mechanisms.

• Interdisciplinary Bio Central
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• v.2 no.2
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• pp.6.1-6.5
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• 2010

Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.

• Proceedings of the KSME Conference
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• 2008.11a
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• pp.1928-1933
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• 2008

In this paper, elastic properties such as Young's modulus and Poisson's ratio of various transition metal nanofilms are calculated for the {100} and {110} surfaces by using molecular dynamics simulation. A new method using $3^{rd}$ order elastic constants and least square method is presented for the calculation of elastic constants. We also introduce analytical method of calculating elastic constants for EAM potential and it's results as the reference value to be compared with the simulation results.

• International Journal of Air-Conditioning and Refrigeration
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• v.9 no.2
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• pp.8-18
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• 2001

The direct simulation Monte Carlo Method is applied to investigate the two-dimensional flow fields of a turbomolecular pump(TMP) in both molecular and transition flow regions. The pumping characteristics of the TMP are investigated for a wide range of the Knudsen number. The maximum of compression ratio and of pumping speed strongly depend on the Knudsen number in transition region, while they weakly depend on the Knudsen number in free molecular flow region. The present numerical results show good agreement with the previously known experimental data. Finally. the results of the single blade row in both molecular and transition regions are used to predict the overall performance of a TMP, which has three kinds of blade with 24-rows.

• Macromolecular Research
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• v.11 no.3
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• pp.146-151
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• 2003

The dependence of electrical conductivity on concentrations of diallyldimethylammonium chloride (DADMAC) monomer, linear poly(DADMAC) and their mixture monomer/poly(DADMAC) in dilute aqueous solution exhibits a linear relationship. It was possible to calculate conversion of DADMAC polymerization by measuring its electric conductivity. Although the electrical conductivity of the poly(DADMAC) solution decreased with increasing its molecular weight, in the process of UV or ionizing radiation polymerization the molecular weight of the polymers could be kept constant in the case of fixed temperature, UV-luminous intensity or dose rate. Based on the method mentioned above, the kinetics of UV induced polymerization of DADMAC in aqueous solution was studied; the overall activation energy of polymerization of DADMAC in the water phase was calculated to be 18.8 kJ mol$^{-1}$ . ${\gamma}$-Radiation-induced polymerization of DADMAC in aqueous solution as a function of absorbed dose was studied as well. The conversion of DADMAC increased quickly with dose before 30 kGy and then increased slowly. The experimental data of both UV- and ${\gamma}$-induced polymerization were verified to be reliable by inverted ultracentrifugation method.