• Bulletin of the Korean Chemical Society
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• v.24 no.11
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• pp.1590-1598
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• 2003

In this paper we have presented the results for viscosity and self-diffusion constants of model systems for four liquid n-alkanes ($C_{12}, C_{20}, C_{32}, and C_{44}$) in a canonical ensemble at several temperatures using molecular dynamics (MD) simulations. The small chains of these n-alkanes are clearly $<{R_{ee}}^2>/6<{R_g}^2>>1$, which leads to the conclusion that the liquid n-alkanes over the whole temperatures considered are far away from the Rouse regime. Calculated viscosity ${\eta}$ and self-diffusion constants D are comparable with experimental results and the temperature dependence of both ${\eta}$ and D is suitably described by the Arrhenius plot. The behavior of both activation energies, $E_{\eta}$ and $E_D$, with increasing chain length indicates that the activation energies approach asymptotic values as n increases to the higher value, which is experimentally observed. Two calculated monomeric friction constants ${\zeta}$ and ${\zeta}_D$ give a correct qualitative trend: decrease with increasing temperature and increase with increasing chain length n. Comparison of the time auto-correlation functions of the end-to-end vector calculated from the Rouse model for n-dodecane ($C_{12}$) at 273 K and for n-tetratetracontane ($C_{44}$) at 473 K with those extracted directly from our MD simulations confirms that the short chain n-alkanes considered in this study are far away from the Rouse regime.

• Bulletin of the Korean Chemical Society
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• v.26 no.4
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• pp.553-557
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• 2005

The formation of striped phases of unsymmetric hexyl octadecyl disulfide ($CH_3(CH_2)_5SS(CH_2)_{17}CH_3$, HOD) and 1-hydroxyundecyl octadecyl disulfide ($CH_3(CH_2)_{17}SS(CH_2)_{11}$OH, HUOD) on Au(111) and graphite has been investigated by scanning tunneling microscopy (STM) to understand the self-assembly processes of dialkyl disulfides. STM imaging clearly shows the formation of striped phases having corrugation periodicities that are nearly consistent with the molecular length of alkanethiolate moieties formed after the S-S bond cleavage of dialkyl disulfide on a gold surface. On the other hand, self-assembled monolayers (SAMs) of dialkyl disulfides on a graphite surface displayed long-range, well-ordered monolayers with one striped pattern that shows periodicity as a function of molecular length via nondissociative adsorption. From a nonoscopic viewpoint, we have clearly demonstrated that dialkyl disulfide SAMs on gold form via S-S bond cleavage of disulfide.

• Bulletin of the Korean Chemical Society
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• v.3 no.2
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• pp.44-49
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• 1982

Dynamic and equilibrium structures of a polymer chain immersed in solvent molecules have been investigated by a molecular dynamic method. The calculation employs the Lennard-Jones potential function to represent the interactions between two solvent molecules (SS) and between a constituent particle (monomer unit) of the polymer chain and a solvent molecule (CS) as well as between two non-nearest neighbor constituent particles of the polymer chain (CC), while the chemical bond for nearest neighbor constituent particles was chosen to follow a harmonic oscillator potential law. The correlation function for the SS, CS and CC pairs, the end-to-end distance square and the radius of gyration square were calculated by varying the chain length (= 5, 10, 15, 20). The computed end-to-end distance square and the radius of gyration square were found to be in a fairly good agreement with the corresponding results from the random-flight model. Unlike earlier works, the present simulation rsesult shows that the autocorrelation function of radius of gyration square decays slower than that of the end-to-end distance square.

• Bulletin of the Korean Chemical Society
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• v.33 no.11
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• pp.3711-3718
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• 2012

Here, we report a chain-length dependent morphology and pore structure tailing of mesoporous silica templated from organogels, which is formed by primary alkylamine and ethylene glycol at room temperature. As the chain length of alkylamine changes from 12 to 18, the resulted materials exhibit a morphology change from layers to spheres and platelets, respectively. SEM and TEM observation revealed that these shapes appear to be inherited from their parent organogels. Further pore structure characterization by nitrogen sorption analysis demonstrates that all the resulted silicas exhibit typical IV isotherms indicative of uniform mesopores, and their pore sizes are dependent on the chain length of alkylamine used.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.222.2-222.2
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• 2002

• Mycobiology
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• v.29 no.1
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• pp.7-10
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• 2001

Based on the rDNA ITS sequences data, specific primer set for PCR detection of wood-decaying fungus Phellinus linteus was designed. The length of PCR products using designed primer set(SHF and SHR) was about 540 bp. Among 11 species, 17 isolates of Phellinus spp. including Phellinus linteus, P. pomaceus, P. spiculosus, P. baumi, P. pini, P. igniarius, P. gilvus, P. biscuspidatus, P. weirii, P. johnsonianus, P. robutus, and P. igniarius, seven isolates of Phellinus linteus showed about 540 bp-sized single band. This molecular technique could offer a useful tool for detecting and identifying Phellinus linteus.

• Bulletin of the Korean Chemical Society
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• v.23 no.11
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• pp.1595-1603
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• 2002

In this paper we have presented the results of diffusion behavior of model systems for eight liquid n-alkanes ($C_{12}$-$C_{44}$) in a canonical (NVT) ensemble at several temperatures using molecular dynamics simulations. For these n-alkanes of small chain length n, the chains are clearly <$R_{ee}^2$>/6<$R_g^2$>>1 and non-Gaussian. This result implies that the liquid n-alkanes over the whole temperatures considered are far away from the Rouse regime, though the ratio becomes close to the unity as n increases. Calculated self-diffusion constants $D_{self}$ are comparable with experimental results and the Arrhenius plot of self-diffusion constants versus inverse temperature shows a different temperature dependence of diffusion on the chain length. The global rotational motion of n-alkanes is examined by characterizing the orientation relaxation of the end-to-end vector and it is found that the ratio ${\tau}1/{\tau}2$ is less than 3, the value expected for a isotropically diffusive rotational process. The friction constants ${\xi}$of the whole molecules of n-alkanes are calculated directly from the force auto-correlation (FAC) functions and compared with the monomeric friction constants ${\xi}_D$ extracted from $D_{self}$. Both the friction constants give a correct qualitative trends: decrease with increasing temperature and increase with increasing chain length. The friction constant calculated from the FAC's decreases very slowly with increasing temperature, while the monomeric friction constant varies rapidly with temperature. By considering the orientation relaxation of local vectors and diffusion of each site, it is found that rotational and translational diffusions of the ends are faster than those of the center.

• Proceedings of the Korean Society of Dyers and Finishers Conference
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• 2008.04a
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• pp.120-122
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• 2008

Relationship between hydrophobicity of dyes and affinity onto pure polypropylene fibers has been analyzed by using the molecular descriptor as a method to predict chemical and physical characteristics of compounds. Hydrophobicity of newly synthesized red dyes calculated by LogP which is one of molecular descriptors was increased continuously as the length of alkyl substituents increased. The dyeability onto polypropylene fibers was increased as LogP of the dyes increased and was very high when the hydrophobicity is over 6.

• BMB Reports
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• v.45 no.11
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• pp.604-611
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• 2012

Recent advances in genome and transcriptome analysis have enabled identification of numerous members of a new class of noncoding RNA, long noncoding RNA (lncRNA). lncRNAs are broadly defined as RNA molecules greater than 200 nt in length and lacking an open reading frame. Recent studies provide evidence that lncRNAs play central roles in a wide range of cellular processes through interaction with key component proteins in the gene regulatory system, and that alteration of their cell- or tissue-specific expression and/or their primary or secondary structures is thought to promote cell proliferation, invasion and metastasis. The biological and molecular characteristics of the large majority of lncRNAs remains unknown, and it is anticipated that improved understanding of the roles played by lncRNAs in cancer will lead to the development of novel biomarkers and effective therapeutic strategies.

• Journal of the Korean Chemical Society
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• v.58 no.6
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• pp.513-516
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• 2014

We measure the conductance of a 4,4'-diaminobiphenyl formed with Ni electrodes using a scanning tunneling microscope-based break-junction technique. For comparison, we use Au or Ag electrodes to form a metal-molecular junction. For molecules that conduct through the highest occupied molecular orbital, junctions formed with Ni show similar conductance as Au and are more conductive than those formed with Ag, consistent with the higher work function for Ni or Au. Furthermore, we observe that the measured molecular junction length that is formed with the Ni or Au electrodes was shorter than that formed with the Ag electrodes. These observations are attributed to a larger gap distance of the Ni or Au electrodes compared to that of the Ag electrodes after the metal contact ruptures. Since our work allows us to measure the conductance of a molecule formed with various electrodes, it should be relevant to molecular electronics with versatile materials.