• 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.

• Journal of The Korean Association For Science Education
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• v.9 no.2
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• pp.13-27
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• 1989

A curriculum for teaching materials in Science Education was studied as a model for modified experiment on fundamental courses. Conscious effort can be made to desingn experiments that require minimum apparatus: that require low-cost equipment that can be made from cheap locally available materials. Computer-aided instruction programs at high school, freshman course level have been developed. The software package was consist of five programs: The program contains explanation and problems for the calculation of resonance energy, molecular structure, mole concept. Rutherford's experiment. thermodynamic processes. Special course equipment package explanation mole concept, Rutherford's experiment, thermodynamic processes. Special course were designed in Science Education with the understanding that to a certain extent science values would be covered in all of the modified experiments and program models.

• Genomics & Informatics
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• v.21 no.1
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• pp.14.1-14.4
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• 2023

OncoPrint, the plot to visualize an overview of genetic variants in sequencing data, has been widely used in the field of cancer genomics. However, still, there have been no Python libraries capable to generate OncoPrint yet, a big hassle to plot OncoPrints within Python-based genetic variants analysis pipelines. This paper introduces a new Python package PyOncoPrint, which can be easily used to plot OncoPrints in Python. The package is based on the existing widely used scientific plotting library Matplotlib, the resulting plots are easy to be adjusted for various needs.

• YAKHAK HOEJI
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• v.54 no.1
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• pp.62-66
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• 2010

Benzopyrene is known to be one of the most powerful carcinogens which can build intercalated motif between base pairs in damaged DNA. The dimension of benzopyrene itself is much bigger than any of the DNA bases and thus the question whether the lesion of some base pair by insertion of benzopyrene can happen with or without a dramatic distortion of the helical structure is a highly interesting theme. In this work we used a molecular mechanics simulation using AMBER program package to go into the conformational characteristics. The condition of the insertion process of the benzopyrene motif from minor groove of the starting structure between the base pairs in the internal area of double helix was investigated using the molecular dynamics simulation at elevated temperature.

• The Bulletin of The Korean Astronomical Society
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• v.42 no.1
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• pp.33.1-33.1
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• 2017

Molecular clouds are the sites of stellar birth, and conditions within the clouds control the mode and tempo of star formation. In particular, turbulence largely determines the density and velocity fields, and can affect the gas kinetic temperature as it decays via shocks. However, despite its central role in star formation and many years of study, the properties of turbulence remain poorly understood. As a part of the TRAO key science program, "Mapping turbulent properties of star-forming molecular clouds down to the sonic scale (PI: Jeong-Eun Lee)", we mapped the northern region of the Orion A molecular cloud and the L1688 region of the ${\rho}$ Ophiuchus molecular cloud in 2 sets of lines (13CO 1-0/C18O 1-0 and HCN 1-0/and HCO+ 1-0) using the Taeduk Radio Astronomy Observatory (TRAO) 14-m telescope. We analyze these maps using a python package 'Turbustat', a toolkit which contains 16 different turbulent statistics. We will present the preliminary results of our TRAO observations and various turbulence statistical analyses.

• Bulletin of the Korean Chemical Society
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• v.34 no.1
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• pp.179-187
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• 2013

We describe newly developed software named KPACK for relativistic electronic structure computation of molecules containing heavy elements that enables the two-component ab initio calculations in Kramers restricted and unrestricted formalisms in the framework of the relativistic effective core potential (RECP). The spin-orbit coupling as relativistic effect enters into the calculation at the Hartree-Fock (HF) stage and hence, is treated in a variational manner to generate two-component molecular spinors as one-electron wavefunctions for use in the correlated methods. As correlated methods, KPACK currently provides the two-component second-order M${\o}$ller-Plesset perturbation theory (MP2), configuration interaction (CI) and complete-active-space self-consistent field (CASSCF) methods. Test calculations were performed for the ground states of group-14 elements, for which the spin-orbit coupling greatly influences the determination of term symbols. A categorization of three procedures is suggested for the two-component methods on the basis of spin-orbit coupling manifested in the HF level.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2004.11a
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• pp.218-221
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• 2004

The electronic state of ZnO doped with Al, Ga and In, which belong to III family elements in periodic table, was calculated using the density functional theory. In this study, the program used for the calculation on theoretical structures of ZnO and doped ZnO was Vienna Ab-initio Simulation Package (VASP), which is a sort of pseudo potential method. The detail of electronic structure was obtained by the describe variational $X{\alpha}(DV-X{\alpha})$(DV-Xa) method, which is a sort of molecular orbital full potential method. The optimized crystal structures obtained by calculations were compared to the measured structure. The density of state and energy levels of dopant elements was shown and discussed in association with properties.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.4
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• pp.467-476
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• 2019

Objective: This research was conducted to study the genetic diversity in several Indonesian cattle breeds using microsatellite markers to classify the Indonesian cattle breeds. Methods: A total of 229 DNA samples from of 10 cattle breeds were used in this study. The polymerase chain reaction process was conducted using 12 labeled primers. The size of allele was generated using the multiplex DNA fragment analysis. The POPGEN and CERVUS programs were used to obtain the observed number of alleles, effective number of alleles, observed heterozygosity value, expected heterozygosity value, allele frequency, genetic differentiation, the global heterozygote deficit among breeds, and the heterozygote deficit within the breed, gene flow, Hardy-Weinberg equilibrium, and polymorphism information content values. The MEGA program was used to generate a dendrogram that illustrates the relationship among cattle population. Bayesian clustering assignments were analyzed using STRUCTURE program. The GENETIX program was used to perform the correspondence factorial analysis (CFA). The GENALEX program was used to perform the principal coordinates analysis (PCoA) and analysis of molecular variance. The principal component analysis (PCA) was performed using adegenet package of R program. Results: A total of 862 alleles were detected in this study. The INRA23 allele 205 is a specific allele candidate for the Sumba Ongole cattle, while the allele 219 is a specific allele candidate for Ongole Grade. This study revealed a very close genetic relationship between the Ongole Grade and Sumba Ongole cattle and between the Madura and Pasundan cattle. The results from the CFA, PCoA, and PCA analysis in this study provide scientific evidence regarding the genetic relationship between Banteng and Bali cattle. According to the genetic relationship, the Pesisir cattle were classified as Bos indicus cattle. Conclusion: All identified alleles in this study were able to classify the cattle population into three clusters i.e. Bos taurus cluster (Simmental Purebred, Simmental Crossbred, and Holstein Friesian cattle); Bos indicus cluster (Sumba Ongole, Ongole Grade, Madura, Pasundan, and Pesisir cattle); and Bos javanicus cluster (Banteng and Bali cattle).

• Korean Journal of Microbiology
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• v.32 no.3
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• pp.177-181
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• 1994

The sequences of the cytoplasmic 5S rRNAs(EMBL accession number X73589 and X73890) from two polupores, Ganoderma applanatum and Schizopora paradoxa, were determined by the direct chemical method for sequencing RNA and compared to the sequences of 9 reported mushrooms. 5S rRNAs of Ganoderma applanatum and Schizopora paradoxa consisted of 118 bases and fit the secondary structure model of the 5S rRNAs of basidiomycetes proposed by Huysmans et al. Based on Kimura’s K_nuc values, the closest fungus to Ganoderma applanatum was Ceratobasidium cornigerum and the one to Schizopora paradoxa was Bjerkandera adusta. When the secondary structures of 5S rRNAs of 11 mushrooms were compared the base substitution occurred at helix regions more than at loop regions. When a phylogenetic tree was constructed using the Neighbor program of the PHYLIP package, it partially discriminated and separated the mushrooms of the Hymenomycetes by the order.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2005.07a
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• pp.172-173
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• 2005

The electronic state of ZnO doped with Y was calculated using the density functional theory. In this study, the program used for the calculation on theoretical structures of ZnO and doped ZnO was Vienna Ab-initio Simulation Package (VASP), which is a sort of pseudo potential method. The detail of electronic structure was obtained by the descrite variational $X\alpha$ (DV-$X\alpha$) method, which is a sort of molecular orbital full potential method. The optimized crystal structures obtained by calculations were compared to the measured structure. The density of state and energy levels of dopant elements was shown and discussed in association with optical properties.