• Polymer(Korea)
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• v.35 no.6
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• pp.513-519
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• 2011

Molecular simulations via the molecular dynamics method have been carried out to investigate the dynamic collision properties of penetrable-sphere model fluids. The collision frequencies, the mean free paths, the angle distributions of the hard-type reflection and the soft-type penetration, and the effective packing fractions are computed over a wide range of the packing fraction ${\phi}$ and the repulsive energy ${\varepsilon}^*$. The soft-type collisions are dominated for lower repulsive energy systems, while the hardtype collisions for higher repulsive energy systems. Very interestingly, the ratio of the soft-type (or, the hard-type) collision frequency to the total collision frequency is directly related with the Boltzmann factor of acceptance (or rejection) probabilities in the canonical ensemble Monte Carlo calculations. Such dynamic collision properties are shown to be restricted for highly repulsive and dense systems of ${\varepsilon}^*{\geqq}3.0 $and ${\phi}{\geqq}0.7$, indicating the cluster forming structures in the penetrable-sphere model.

• Macromolecular Research
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• v.8 no.6
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• pp.292-297
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• 2000

The theoretical synthesis of the isotactic and syndiotactic poly(methyl methacrylate) were carried out as a model for real polymerization reactions following the normal chain reaction processes by repeating the uniform localization of wave functions with inclusion of the interaction between the end group of the cluster and an attaching molecule by the elongation method, and then, the calculated value was compared with the usual PM$_3$ calculation. The results revealed that a reaction of cluster with monomer molecules has made it possible to calculate the electronic structure and total energy of polymer with nearly infinite length and a matrix of constant dimension. The isotactic poly(methyl methacrylate) is more stable than syndiotactic one. The same tendency have been found between the experimentally measured properties and a calculated total energy to explain the chain motion in isotatic and syndiotactic poly(methyl methacrylate).

• BMB Reports
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• v.49 no.7
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• pp.355-356
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• 2016

The THO/TREX complex consists of several conserved subunits and is required for mRNA export. In metazoans, THO/TREX binds a subset of mRNAs during RNA splicing, and facilitates their nuclear export. How THO/TREX selects RNA targets is, however, incompletely understood. In our recent study, we reported that THO is loaded onto Piwi-interacting RNA (piRNA) precursor transcripts independent of splicing, and facilitates convergent transcription in Drosophila ovary. The precursors are later processed into mature piRNAs, small noncoding RNAs that silence transposable elements (TEs). We observed that piRNAs originating from dual-strand clusters, where precursors are transcribed from both strands, were specifically affected by THO mutation. Analysis of THO-bound RNAs showed enrichment of dual-strand cluster transcripts. Interestingly, THO loading onto piRNA precursors was dependent on Cutoff (Cuff), which comprises the Rhino-Deadlock-Cutoff (RDC) complex that is recruited to dual-strand clusters by recognizing H3K9me3 and licenses convergent transcription from he cluster. We also found that THO mutation affected transcription from dual-strand clusters. Therefore, we concluded that THO/TREX is recruited to dual-strand piRNA clusters, independent of splicing events, via multi-protein interactions with chromatin structure. Then, it facilitates transcription likely by suppressing premature termination to ensure adequate expression of piRNA precursors.

• Bulletin of the Korean Chemical Society
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• v.15 no.7
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• pp.545-549
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• 1994

Using the extended Hackel molecular orbital method in connection with the tight binding model, we have studied electronic structure and related properties of the charged cluster models relating to superconducting $YBa_{2}Cu_{3}O_{7-x}$, crystals in which O-atoms in regular sites were selectively replaced with Se atoms. In analogy to the isomorphism problem with molecules, we discuss all possible combinations of Se-substitutions in O-sites with one, two, and four Se atoms. The calculations are carried out within charged cluster models for analogues of YBa-copper oxide. Our results suggest that the electronic structure of the symmetrically Se-substituted or Se-added compound is closer to that of the YBCO superconducting compound than that obtained from the unsymmetrical substitution. This applies in particular if O is replaced with Se around the Cu(1) site. Symmetrical substitutions in the $CuO_2$ layers give rise to large variations in the electronic structure of $YBa_{2}Cu_{3}O_{7}$. This is consistent with the fact that superconductivity is very sensitive to the electronic population of the $CuO_2$ layers.

• Korean Journal of Breeding Science
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• v.42 no.1
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• pp.11-22
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• 2010

The population structure of a domesticated species is influenced by the natural history of the populations of its pre-domesticated ancestors, as well as by the breeding system and complexity of breeding practices implemented by humans. In the genetic and population structure analysis of 122 South Asia collections using 29 simple sequence repeat (SSR) markers, 362 alleles were detected, with an average of 12.5 per locus. The average expected heterozygosity and polymorphism information content (PIC) for each SSR locus were 0.74 and 0.72,respectively. The model-based structure analysis revealed the presence of three clusters with the 91.8% (shared > 75%) membership, with 8.2% showing admixture. The genetic distances of Clusters 1-3 were 0.55, 0.56, and 0.68, respectively. Polymorphic information content followed the same trend (Cluster 3 had the highest value and Cluster 1 had smallest value), with genetic distances for each cluster of 0.52, 0.52, and 0.65, respectively. This result could be used for supporting rice breeding programs in South Asia countries.

• Proceedings of the Korean Vacuum Society Conference
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• 2000.02a
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• pp.157-157
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• 2000

The adsorption processes of methyl chloride on Si(100)-2$\times$1 have been studied by low energy electron diffraction (LEED), Auger electron spectroscopy (AES) and semiempirical PM3 calculations. The dissociative adsorption of the methyl chloride on Si(100) takes place without breaking of the silicon dimer with high efficiency. For adsorption at the room temperature, the existence of a precursor state is confirmed by the behavior of the sticking probability depending on the coverage and temperature. From AES measurements, the determined activation barrier of adsorption ($\Delta$ Hads) is -28.4 kj/mol. This results indicate that the dissociative process is nonactivated. The optimized precursor state of CH3Cl on the Si(100)-2$\times$1 surface was determined by PM3 calculations based on a cluster model.

• The Bulletin of The Korean Astronomical Society
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• v.40 no.1
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• pp.58.3-59
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• 2015

Dynamical expansion of H II regions plays a key role in dispersing surrounding gas and therefore in limiting the efficiency of star formation in molecular clouds. We use analytic methods and numerical simulations to explore expansions of spherical dusty H II regions, taking into account the effects of direct radiation pressure, gas pressure, and total gravity of the gas and stars. Simulations show that the structure of the ionized zone closely follows Draine (2011)'s static equilibrium model in which radiation pressure acting on gas and dust grains balances the gas pressure gradient. Strong radiation pressure creates a central cavity and a compressed shell at the ionized boundary. We analytically solve for the temporal evolution of a thin shell, finding a good agreement with the numerical experiments. We estimate the minimum star formation efficiency required for a cloud of given mass and size to be destroyed by an HII region expansion. We find that typical giant molecular clouds in the Milky Way can be destroyed by the gas-pressure driven expansion of an H II region, requiring an efficiency of less than a few percent. On the other hand, more dense cluster-forming clouds in starburst environments can be destroyed by the radiation pressure driven expansion, with an efficiency of more than ~30 percent that increases with the mean surface density, independent of the total (gas+stars) mass. The time scale of the expansion is always smaller than the dynamical time scale of the cloud, suggesting that H II regions are likely to be a dominant feedback process in protoclusters before supernova explosions occurs.

• Bulletin of the Korean Chemical Society
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• v.14 no.1
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• pp.132-137
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• 1993

The electronic structure of two dimensional layered compound, FeOCl, is studied with the band model and the cluster model approximation employing Extended-Huckel (EH) method. We examine the effects of intercalation (e.g., localization of transferred electron, conductivity increase). FeOCl has the electronic structure typical for layered compounds as expected. For FeOCl-$Li_{1/2}$ system, the charge transfer from Li to the FeOCl lattice occurs, and electrons are built up almost exclusively on Fe atoms. The partially filled band of FeOCl-$Li_{1/2}$ complex is responsible for the increase in conductivity.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2003.11a
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• pp.148-151
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• 2003

The spin density of ${\beta}-MnO_2$ structure was theoretically investigated by $DV-X_{\alpha}$ (the discrete variation $X{\alpha}$) method, which is a sort of the first principle molecular orbital method using Hatre-Fock-Slater approximation. The used cluster model was $[Mn_{14}O_{56}]^{-52}$. The ${\beta}-MnO_2$ is a paramagnetic oxide semiconductor material having the energy band gap of 0.18 eV and an 3 loan-pair electrons in the 3d orbital of an cation. This material exhibits spin-only magnetism and has the magnetic ordering temperature of 94 K. Below this temperature its magnetism appears as antiferromagnetism. The calculations of electronic state showed that if the initial spin condition of input parameters changed, the magnetic state changed from paramagnetic to antiferromagnetic. When d orbital of all Mn atoms in cluster had same initial spin state as only up spin, paramagnetic spin density distribution appeared by the calculation. On the other way, d orbital had alternately changed spin state along special direction the resulted spin distribution showed antiferromagnetism.

• Korean Journal of Crystallography
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• v.14 no.1
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• pp.16-23
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• 2003

The electronic structure and chemical bonding of β-MnO₂ were theoretically investigated by DV-X/sub α/ (the discrete variation X/sub α/) method. which is a sort of the first principle molecular orbital method using Hatre-Fock-Slater approximation. The calculations on several cluster models having different sizes were carried out for the determination of a model suited for analyzing bulk state. The Mn/sub 15/O/sub 56/ model was selected as a sufficiently suitable model for the calculation of electronic state and chemical bonding by the comparison of the calculated XPS (X-ray photo-electron spectrum) and experimentally measured XPS. By using this model, the electron energy level, the density of state, the bond overlap population, the charge density distribution, and the net ionic transfer between cations and anions were calculated and discussed.