• Title/Summary/Keyword: Molecular clusters

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From Gas Phase Clusters to Nanomaterials: An Overview of Theoretical Insights

  • Kim, Kwang-S.
    • Bulletin of the Korean Chemical Society
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    • v.24 no.6
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    • pp.757-762
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    • 2003
  • Since theoretical investigations of gas phase clusters enable the evaluation of intrinsic molecular properties and intermolecular interactions, one can predict the macroscopic properties of bulk matter, from a microscopic determination of the properties of individual atoms, molecules, or clusters. Based on the insights obtained from theoretical investigations of the properties of a large number of cluster systems (ranging from simple water clusters to large π-systems), we have investigated the properties of various novel molecular systems including endo/exohedral fullerenes, nanotori, nonlinear optical materials, ionophores/receptors, polypeptides, enzymes, organic nanotubes, nanowires, and electronic and nano-mechanical molecular devices. The present minireview highlights some of the interesting results obtained in the course of our extensive theoretical investigations of clusters and nanomaterials.

Numerical Classification of Actinomycetes Isolated from Volcanic Soil

  • Kim, Seung-Bum;Lee, Soon-Dong;Kim, Seon-Young;Oh, Hyung-Myung;Kang, Sa-Ouk
    • Journal of Microbiology
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    • v.34 no.2
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    • pp.105-116
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    • 1996
  • Of actinomycetes isolated from volcanic compost soils, 115 representative strains which showed distinctive morphologicla features were numerically classified, compared with reference strains of Streptomyces. One hundred and twenty unit characters were tested and the average probability of error was 4.27%. The cluster analysis resulted in two groups: group A included strains of actinomycetes except streptomycetes. Group A was divided into 2 major clusters (over 5 strains), 10-diaminopimelic acid. Group B was divided into 5 clusters, of which 4 clusters contained mesodiminopimelic acid and 1 cluster LL-diaminopimelic acid. The major clusters of group A showed higher abilities of substrate utilization and degradation, and higher resistance to inhibitors, whereas the minor and single member clusters of group A showed relatively higher antimicrobial activities. On the other hand, all clusters of group B showed relatively lower abilities of substrate utilization and degradation and lower resistance to inhibitors.

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Molecular Dynamics Simulations of Small n-Alkane Clusters in a Mesoscopic Solvent

  • Ko, Seo-Young;Lee, Song-Hi
    • Bulletin of the Korean Chemical Society
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    • v.24 no.6
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    • pp.771-776
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    • 2003
  • The structural and dynamic properties of small n-alkane clusters embedded in a mesoscopic solvent are investigated. The solvent interactions are taken into account through a multi-particle collision operator that conserves mass, momentum and energy and the solvent dynamics is updated at discrete time intervals. The cluster molecules interact among themselves and with the solvent molecules through intermolecular forces. The properties of n-heptane and n-decane clusters interacting with the mesoscopic solvent molecules through repulsive Lennard-Jones interactions are studied as a function of the number of the mesoscopic solvent molecules. Modifications of both the cluster and solvent structure as a result of cluster-solvent interactions are considered. The cluster-solvent interactions also affect the dynamics of the small n-alkane clusters.

Molecular Dynamics Simulations of the Diffusion of Bimetallic Nanoclusters Supported on Graphite (분자동역학을 이용한 흑연 위에서의 2종 합금 나노입자의 확산 거동 연구)

  • Park, Joon Woo;Lee, Ju Seong;Min, Chan Ho;Lee, Hyun Seok;Ryu, Ji Hoon;Seo, Dong Hwa;Lee, Hyuck Mo
    • Korean Journal of Metals and Materials
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    • v.47 no.8
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    • pp.461-465
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    • 2009
  • We study the diffusion of Ag based bimetallic nanoclusters supported on graphite. Using a molecular dynamics simulation, we reveal that the Ag clusters show rapid diffusion because of their hexagonal bottom layer. In order to decrease the rate of diffusion, we added Pt and Ni to distort the structure of the alloy cluster (i.e., the alloying method). We expected Pt to provide a stronger force on Ag atoms, and Ni to shorten the bond length and thereby change the structure of Ag cluster. However, the attempt was unsuccessful, because Pt and Ni atoms formed cores inside the Ag clusters. We therefore designed a collision system where large Ag clusters collide with small Pt or Ni clusters. Upon collision with Pt clusters, the diffusion showed little change, because Pt atoms are substituted at the Ag atomic site and form a perfectly ordered structure. The collision with Ni, however, deforms the bottom layer as well as the overall cluster structure and decreases diffusion. This outcome appoints toward the possibility of further application to the manufacture of durable nanocatalysts.

Surface Phenomena of Molecular Clusters by Molecular Dynamics Method (분자운동력학법에 의한 분자괴의 표면현상)

  • Maruyama, Shigeo;Matsumoto, Sohei;Ogita, Akihiro
    • Journal of Advanced Marine Engineering and Technology
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    • v.20 no.3
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    • pp.11-18
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    • 1996
  • Liquid droplets of water and argon surrounded by their vapor have been simulated by the milecular dynamics method. To explore the surface phenomena of clusters, each molecule is classified into 'liquid', 'surface', or 'vapor' with respect to the number of neighbor molecules. The contribution of a 'surface' molecule of the water cluster to the far infrared spectrum is almist the same as that of the 'liquid' molecule. Hence, the liquid-vapor interface is viewed as geometrically and temporally varying boundary of 'liquid' molecules with only a single layer of 'surface' molecules that might have different characteristics from the 'liquid' molecules. The time scale of the 'phase change' of each molecule is estimated for the argon cluster by observing the instantancous kinetic and potential energies of each molecule. To compare the feature of clusters with macroscopic droplets, the temperature dependence of the surface tension of the argon cluster is estimated.

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ReaxFF and Density Functional Theory Studies of Structural and Electronic Properties of Copper Oxide Clusters

  • Baek, Joo-Hyeon;Bae, Gyun-Tack
    • Journal of the Korean Chemical Society
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    • v.64 no.2
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    • pp.61-66
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    • 2020
  • In this study, we investigate the structural and electronic properties of copper oxide clusters, CunOn (n = 9 - 15). To find the lowest energy structures of copper oxide clusters, we use ReaxFF and density functional theory calculations. We calculate many initial copper oxide clusters using ReaxFF quickly. Then we calculate the lowest energy structures of copper oxide clusters using B3LYP/LANL2DZ model chemistry. We examine the atomization energies per atom, average bond angles, Bader charges, ionization potentials, and electronic affinities of copper oxide clusters. In addition, the second difference in energies is investigated for relative energies of copper oxide clusters.

Primary damage of 10 keV Ga PKA in bulk GaN material under different temperatures

  • He, Huan;He, Chaohui;Zhang, Jiahui;Liao, Wenlong;Zang, Hang;Li, Yonghong;Liu, Wenbo
    • Nuclear Engineering and Technology
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    • v.52 no.7
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    • pp.1537-1544
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    • 2020
  • Molecular dynamics (MD) simulations were conducted to investigate the temperature effects on the primary damage in gallium nitride (GaN) material. Five temperatures ranging from 300 K to 900 K were studied for 10 keV Ga primary knock-on atom (PKA) with inject direction of [0001]. The results of MD simulations showed that threshold displacement energy (Ed) was affected by temperatures and at higher temperature, it was larger. The evolutions of defects under various temperatures were similar. However, the higher temperature was found to increase the peak number, peak time, final time and recombination efficiency while decreasing the final number. With regard to clusters, isolated point defects and little clusters were common clusters and the fraction of point defects increased with temperature for vacancy clusters, whereas it did not appear in the interstitial clusters. Finally, at each temperature, the number of Ga interstitial atoms was larger than that of N and besides that, there were other different results of specific types of split interstitial atoms.

Optimal Combination of VNTR Typing for Discrimination of Isolated Mycobacterium tuberculosis in Korea

  • Lee, Jihye;Kang, Heeyoon;Kim, Sarang;Yoo, Heekyung;Kim, Hee Jin;Park, Young Kil
    • Tuberculosis and Respiratory Diseases
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    • v.76 no.2
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    • pp.59-65
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    • 2014
  • Background: Variable-number tandem repeat (VNTR) typing is a promising method to discriminate the Mycobacterium tuberculosis isolates in molecular epidemiology. The purpose of this study is to determine the optimal VNTR combinations for discriminating isolated M. tuberculosis strains in Korea. Methods: A total of 317 clinical isolates collected throughout Korea were genotyped by using the IS6110 restriction fragment length polymorphism (RFLP), and then analysed for the number of VNTR copies from 32 VNTR loci. Results: The results of discriminatory power according to diverse combinations were as follows: 25 clusters in 83 strains were yielded from the internationally standardized 15 VNTR loci (Hunter-Gaston discriminatory index [HGDI], 0.9958), 25 clusters in 65 strains by using IS6110 RFLP (HGDI, 0.9977), 14 clusters in 32 strains in 12 hyper-variable VNTR loci (HGDI, 0.9995), 6 clusters in 13 strains in 32 VNTR loci (HDGI, 0.9998), and 7 clusters in 14 strains of both the 12 hyper-variable VNTR and IS6110 RFLP (HDGI, 0.9999). Conclusion: The combination of 12 hyper-variable VNTR typing can be an effective tool for genotyping Korean M. tuberculosis isolates where the Beijing strains are predominant.

SECONDARY ELECTRONS IN CLUSTERS OF GALAXIES AND GALAXIES

  • HWANG CHORNG- YUAN
    • Journal of The Korean Astronomical Society
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    • v.37 no.5
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    • pp.461-463
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    • 2004
  • We investigate the role of secondary electrons in galaxy clusters and in ultra-luminous infrared galaxies (ULIGs). The radio emission in galaxy clusters and ULIGs is believed to be produced by the synchrotron radiation of relativistic electrons. Nonetheless, the sources of these relativistic electrons are still unclear. Relativistic secondary electrons can be produced from the hadronic interactions of cosmic-ray nuclei with the intra-cluster media (ICM) of galaxy clusters and the dense molecular clouds of ULIGs. We estimate the contribution of the secondary electrons in galaxy clusters and ULIGs by comparing observational results with theoretical calculations for the radio emission in these sources. We find that the radio halos of galaxy clusters can not be produced from the secondary electrons; on the other hand, at least for some ULIGs, the radio emission can be dominated by the synchrotron emission of the secondary electrons.

Genetic Analysis and Serological Detection of Novel O-Antigen Gene Clusters of Plesiomonas shigelloides

  • Wang, Xiaochen;Xi, Daoyi;Li, Yuehua;Yan, Junxiang;Zhang, Jingyun;Guo, Xi;Cao, Boyang
    • Journal of Microbiology and Biotechnology
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    • v.31 no.4
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    • pp.520-528
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    • 2021
  • Plesiomonas shigelloides, a member of the family Vibrionaceae, is a gram-negative, rod-shaped, facultative anaerobic bacterium with flagella. P. shigelloides has been isolated from such sources as freshwater, surface water, and many wild and domestic animals. P. shigelloides contains 102 O-antigens and 51 H-antigens. The diversity of O-antigen gene clusters is relatively poorly understood. In addition to O1 and O17 reported by other laboratories, and the 12 O serogroups (O2, O10, O12, O23, O25, O26, O32, O33, O34, O66, O75, and O76) reported previously by us, in the present study, nine new P. shigelloides serogroups (O8, O17, O18, O37, O38, O39, O44, O45, and O61) were sequenced and annotated. The genes for the O-antigens of these nine groups are clustered together in the chromosome between rep and aqpZ. Only O38 possesses the wzm and wzt genes for the synthesis and translocation of O-antigens via the ATP-binding cassette (ABC) transporter pathway; the other eight use the Wzx/Wzy pathway. Phylogenetic analysis using wzx and wzy showed that both genes are diversified. Among the nine new P. shigelloides serogroups, eight use wzx/wzy genes as targets. In addition, we developed an O-antigen-specific PCR assay to detect these nine distinct serogroups with no cross reactions among them.