• Bulletin of the Korean Chemical Society
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• 제25권7호
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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.

• 한국과학교육학회지
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• 제9권2호
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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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• 제21권1호
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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.

• 약학회지
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• 제54권1호
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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.

• 천문학회보
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• 제42권1호
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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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• 제34권1호
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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.

• 한국전기전자재료학회:학술대회논문집
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• 한국전기전자재료학회 2004년도 추계학술대회 논문집 Vol.17
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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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• 제32권4호
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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).

• 미생물학회지
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• 제32권3호
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• pp.177-181
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• 1994

담자균류 균심류의 영지과에 속하는 잔나비걸상(Ganoderma applanatum)과 구멍장이 버섯과에 속하는 좀구멍버섯 (Schizopora paradoxa) 두 종의 5S rRNA 염기서열들을 (EMBL accession mumbers X73589 and X73890) directchemical method로 분석 결정하고 담자균류 균심류와 복균류의 기존에 밝혀진 9종 버섯의 염기서열과 비교하였다. 잔나비걸상과 좀구멍버섯의 5S rRNA는 각각 118개의 염기로 구성되어 있으며 B형 5S rRNA에 해당하였고 Huysmans 등이 제시한 2차구조의 모델에 들어 맞으며 Walker와 Doolittle이 제시한 제 5 염기서열군에 속하였다. 진화거리를 나타내는 Kimura의 염기치환상수 $K_{nuc}$값에 으하면 잔나비걸상과 가장 가까운 좋은 고약버석과의 Ceratobasidium cornigerum으로서 염기 3개의 차이를 보였으며 좀구멍버섯과 가장 가까운 좋은 구멍장이 보섯과의 줄버섯(Bjerkandera adusta)으로서 염기 두개의 차이를 보였다.11개 5S rRNA의 이차구조를 비교하였을때 염기의 치환은 loop 부분보다는 helix 부분에서 많이 일어났으며, 이는 helix 부분이 loop 부분보다는 진화적으로 덜 보존되어 있고 진화 분지를 형성하는데 보다 많은 영향을 주었음을 시사하였다. Kimura의 two parameter method로 계산된distance matrix를 사용하고 Felsenstein PHYLIP package의 Neighbor program에서 Neighborjpomomg option을 이용하여 계통수를 그렸을 때 균심류의 버섯들은 부분적으로 목별로 구분되었다. 균심류의 민주름버섯목에는 적어도 먹물버섯류(Coprinus radiatus)를 제외한 2개의 계통분지가 있고 주름버섯목에도 2개의 계통 분지가 있으며, 복균류에는 말불버섯(Lycoperdon pyriforme)이 독립된 계통분지를 형성하고 있음을 시사하였다.

• 한국전기전자재료학회:학술대회논문집
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• 한국전기전자재료학회 2005년도 하계학술대회 논문집 Vol.6
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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.