• Journal of Advanced Marine Engineering and Technology
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• v.29 no.1
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• pp.60-67
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• 2005

Generally. in the molecular dynamics simulations. the Verlet neighboring list algorithm is used for the reduction of a simulation time On the other hand. the application of the Verlet neighboring list forces the time evolution of a simulation system to follow an unrealistic path in a phase space. In equilibrium state, it does not matter with the simulation results because the individual molecule's motion is originally random and any effect due to a small deviation from a real time evolution can be completely ignored. However, if an unsteady state is involved. such a deviation may significantly affect to the results. That is, there is a Possibility that the simulation results Provide ones with any misleading data In this study we evaluated the effect due to the Verlet neighboring list in performing the simulation of a non-equilibrium state and suggested the method to avoid it.

• Journal of Advanced Marine Engineering and Technology
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• v.29 no.1
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• pp.34-41
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• 2005

An experimental study of molecular motions on a liquid-vapor interface is limited due to micro-scale characteristics of a system with an angstrom or a nanometer size Therefore, in recent, many studies for micro-scale systems have been conducted by a computer simulation because it is free from experimental limitations. In this study, through the molecular dynamic (MD) method. molecular behavior was clarified on a liquid-vapor interface and a criterion to distinguish between liquid and vapor was suggested by a potential energy and the number of neighboring molecules. At an interface. the potential energy of a molecule was increased but the number of neighboring molecules was decreased when the molecule moved into a vapor region from a liquid region, and vice versa.

• Korean Journal of Crystallography
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• v.9 no.2
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• pp.120-124
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• 1998

N-tert-Butyl-2-(1-acetoxy-2-fluoro-1-butyl)benzenesulfonamide의 분자 및 결정구조를 X-선회절법으로 연구하였다. 결정의 공간군은 P21/c이고, 단위포 상수는 a=8.583(2) , b=14.674(2) , c=14.703(2) , β=103.23(1)0, Z=4, V=1802.6(5) 3, Dc=1.27 Mgm-3이다. 회절반점들의 세기는 Rigaku AFC-5 Diffractometer로 얻었으며, graphite로 단색화한 Cu-KαX-선을 사용하였다. 분자구조는 직접법으로 풀었으며 최소자승법으로 정밀화하였다. 최종신뢰도 R값은 2472개의 회절반점에 대하여 0.069였다. 분자 내에 N(7)과 O(4)사이에 1개의 수소결합[2.990(4) ]을 갖으며, C(14)와 C(15)는 반대배열을 갖고 있다. 분자간 가장 인접한 거리는 3.465(5) [C(19) O(5)] (symmetry code: -x, y+1/2, -z+1/2)로 분자간 접촉은 van der Waals 힘에 의해 결합되어 있다.

• KIPS Transactions on Computer and Communication Systems
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• v.4 no.1
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• pp.1-4
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• 2015

This paper presents an algorithm for finding valid side chain conformations of amino acids, when given channel is transformed. The suggested algorithm implements a protein molecule with flexible side chains based on the flexibility of amino acids, and extracts adjacent amino acids that affect the formation of the channel. We detect the collision between adjacent amino acids and neighbors, in order to exclude invalid side chain conformations. Then, we construct the rotation angle combination tree to choose valid side chain conformations.

• Nuclear Engineering and Technology
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• v.8 no.3
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• pp.159-168
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• 1976

Acrylic acid has been grafted onto nylon fabric with ceric salts and ${\gamma}$-rays from Co-60 as initiators. The distribution of molecular weight of the grafted polyacrylic acid has been determined and it was found that the ratio of weight-average and number-average molecular weight was higher in room temp. than in low temp. (-184$^{\circ}C$). The weight-average molecular weight of the polyacrylic acid was calculated from viscosity measurements in sodium hydroxide solution. The factors affecting graft polymerization of acrylic acid onto nylon were examined. A possible mechanism that the oxidation of nylon probably takes place at the methylene group attached to nitrogen to give a free-radical was discussed.

• Analytical Science and Technology
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• v.12 no.6
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• pp.478-483
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• 1999

Coagulation efficiencies of some organic compounds by aluminum based coagulants including alum, PAC, PACS were studied. The coagulation efficiency was highest at the neutral pH. It was decreased with an order of PACS, PAC, and alum at the neutral pH. The organic compounds of high molecular weights showed good coagulation efficiencies with all coagulants, while the small molecules were not coagulated. Organic compounds having more than two adjacent functional groups of OH and COOH showed coagulation efficiencies of 10~80%.

• Journal of the Korean Chemical Society
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• v.52 no.1
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• pp.7-15
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• 2008

Molecular motion influencing the absorption spectrum of a chromophore in liquid is theoretically described by a quantum mechanical time correlation function. In the present paper, we developed a theoretical method to calculate such a quantum mechanical time-correlation function from a classical time-correlation function using semi-classical approximations. The calculated time-correlation function was combined with the second order cumulant expansion method to calculate the absorption spectrum of nile blue in acetonitrile. Reasonably good agreement with experimental spectrum was obtained. From the comparison with experimental spectrum, we concluded that the time scale of solvation dynamics of the system should be longer then 1ps and the first shell of solvent is the major contribution to the solvation dynamics.

• Journal of the Korean Chemical Society
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• v.33 no.6
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• pp.623-632
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• 1989

The positions and interaction energies of framework atoms and water molecules of $Mn^{2+}$-exchanged zeolite A were calculated using some potential energy functions and an optimization program. The sum of interaction energies of framework atoms in dehydrated $Mn_{4,5}Na_3-A$ was approximately the same as those of thermally stable $Ca^{2+}$-or $Mg^{2+}$-exchanged zeolite A. Since $Mn^{2+}$ ions can form good coordination bonds with framework oxygens even in dehydrated state, $Mn^{2+}$-exchanged zeolite A is considered to be thermally stable. The optimized positions of framework atoms and ions in this work are agreed well with the crystallographic data. Three groups of water molecules are found in hydrated $Mn^{2+}$-exchanged zeolite A; W(I) group of water molecules having only hydrogen bonds, W(II) group coordinated to $Na^+$ ion, and W(III) group coordinated to $Mn^{2+}$ ion. The average binding energy of each group of water molecules decrease in the order of W(III) > W(II) > W(I). The activation energies in the dehydration reaction of each group of water molecules increased in accordance with their binding energy.

• Journal of the Korean Magnetics Society
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• v.3 no.3
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• pp.179-184
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• 1993

The X-ray diffraction pattern of amorphous $Fe_{78}Si_{9}B_{13}$ alloy was analyzed to obtain the radial distribution function (RDF) where the first peak was in the form of Gaussian function. The calculated coordination number of the form of Gaussian functiono The calculated coordination number of the sample is 13.5, the mean distance betweeon near-neighbor atoms $r_{0}$ is $2.595{\AA}$ and a Gaussian parametet ${\delta}r$ indicating near-neighbor atomic distri-bution is $0.27{\AA}$. The temperature dependence of saturated magnetization at low temperature could be explained by spin wave excitations theory yielding the spin wave stiffness constant as $117.8\;meV\;{\AA}^2$. Also, we tried to fit the observed temperature dependence of saturated magnetization with the Handrich's equation of the modified molecular field theory for the amorphous ferromagnet. Nice fittings are obtained when we used the parameters ${\Delta}=0.32$(S=1/2) and ${\Delta}=0.23$(S=1), respectively. Finally, the calculated spin wave stiffness constant using the parameters and the structural data are $149\;meV\;{\AA}^2$ for S=1/2 and $138\;meV\;{\AA}^2$ for S=1, respectively. The mean exchange coupling integral between near-neighbor atoms was estimated to be 17.9 meV for S=1/2 and 6.7 meV for S=1.

• Journal of Plant Biotechnology
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• v.34 no.4
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• pp.347-354
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• 2007

Commercialization of genetically modified (GM) plants will be required the assessment of risks associated with the release of GM plants that should include a detailed risk assessment of their impacts in human health and the environment. Prior to GM plant release, applicants should provide the information on GM crops for approval. We carried out this study to provide the molecular data for risk assessment of the GM Chinese cabbage plants with insect-resistance gene, modified CryIAc, which we obtained by Agrobacterium-transformation. From the molecular analysis with GM Chinese cabbage, we confirmed the transgene copy number and stability, the expression of the transgene, and integration region sequences between the transgene and the Chinese cabbage genome. Based on the unique integration DNA sequences, we designed specific primer set to detect GM Chinese cabbage and set up the GM cabbage detection method by qualitative PCR analysis. Qualitative analysis with GM Chinese cabbage progenies analysis was revealed the same as the result of herbicide treatment. Our results provided the molecular data for risk assessment analysis of GM Chinese cabbage and demonstrated that the primer set proposed could be useful to detect GM Chinese cabbage.