Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 2 , Issue 1
Showing 1-6 articles out of 6 articles from the selected issue
General Papers
  • Tadayosi YOSHIMURA, Yoshihiro AOYAMA, Akinori UEJIMA
    Type: General paper
    2003 Volume 2 Issue 1 Pages 1-6
    Published: 2003
    Released: May 16, 2003
    JOURNALS FREE ACCESS
    The pattern recognition method is used as principal component (PC) analysis in chemistry research on plural sensors systems. The PC score pattern is found from the three-dimensional (3D) data. However, the effective graphical tool for displaying the 3D data is limited. This paper describes the usefulness of the stereo pair in 3D display of the PC data. The scatter diagram of the stereo pair, made by the Excel/VBA macro-program, is useful for the plotting with similar clusters.
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  • Toshiyuki MEGURO, Tadashi ANDO, Ichiro YAMATO
    Type: General paper
    2003 Volume 2 Issue 1 Pages 7-16
    Published: 2003
    Released: May 16, 2003
    JOURNALS FREE ACCESS
    We developed the object-oriented class library "YLO" to study molecular structures. YLO is written in C++ and composed of a set of classes, which are a kind of program units, resembling subroutines in Fortran. Each class performs a certain job independently in a whole program. YLO deals with non-organic, organic molecules and biological macromolecules. The coordinate file of a molecule is read / written in PDB format. Using the YLO library, one can make various types of application programs efficiently, such as Monte Carlo simulator, Genetic Algorithm optimizer and so on.
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  • Akifumi ODA, Shuichi HIRONO
    Type: General paper
    2003 Volume 2 Issue 1 Pages 17-26
    Published: 2003
    Released: May 16, 2003
    JOURNALS FREE ACCESS
    The calculations of atomic charges play important roles in the non-bonded interaction terms of energy functions of molecular mechanics (MM) and molecular dynamics (MD) methods. In this study, we introduce atom types for the charge equilibrium method (QEq method), which can be easily calculated and can derive different charges for different conformations. Since this method requires one-center Coulombic terms and electronegativities as parameters, we determine these parameters by using 153 compounds. We also determined the parameters for carboxylic acid ion carbon, pyrrole nitrogen, ammonium ion nitrogen, nitro nitrogen, furan oxygen, trivalent and quintivalent phosphorus, bivalent and sexivalent sulfur, thiophene sulfur, chlorine and bromine, see Table 3. Using these atom types and parameters, appropriate atomic charges can be obtained for various molecules by the QEq method and, thus, more accurate molecular energy becomes available in MM and MD.
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  • Masanori ITABA, Atsushi MINATO, Satoshi OZAWA, Yosio HIKI
    Type: General paper
    2003 Volume 2 Issue 1 Pages 27-32
    Published: 2003
    Released: May 16, 2003
    JOURNALS FREE ACCESS
    Molecular dynamics computer experiments have been carried out for two-dimensional hexagonal mass-spring model crystals. Anharmonic forces up to the third order were taken into account, and central forces were considered between the nearest neighbor (nn) and the next nearest neighbor (nnn) atoms. The ratio of the potential between the nnn atoms to the potential between the nn atoms was varied. An input pulse displacement was given to central atomic planes in the crystal or to the end atomic plane of the crystal, and induced displacements and velocities of all atoms were computed. Solitons were produced as the atomic excitation, and the propagation velocity and the strength of solitons were enumerated. Two crystallographic directions were taken for the input pulse direction, and the values of the nnn interaction parameters were widely varied. As the nnn interaction was enhanced, the soliton velocity increased and the soliton energy decreased. The results were compared with those of 1D, 2D and 3D crystals obtained previously. Discussions and remarks are presented for these results.
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Technical Papers
  • Kazumitsu SAEKI, Kazutoshi TANABE, Takatoshi MATSUMOTO, Hiroyuki UESAK ...
    Type: Technical paper
    2003 Volume 2 Issue 1 Pages 33-40
    Published: 2003
    Released: May 16, 2003
    JOURNALS FREE ACCESS
    A rapid and intact method has been developed for predicting polyethylene density by near-infrared spectroscopy combined with neural network analysis. Near-infrared spectra in the region of 1.1-2.2 μm wavelength were measured using pellets or powders of twenty-three kinds of polyethylene (PE) with different densities (0.898-0.962 g cm-3). The spectra were used for training a back-propagation neural network after normalized and second-derivative treatments to predict PE density. Although only a small number of spectral data were used for training, a leave-one-out test of neural network analysis has demonstrated good results. In comparison, principal component regression (PCR) analysis and partial least-squares (PLS) regression analysis were applied. The correlation coefficients (R) were calculated to be 1.000, 0.968 and 0.983 for neural network, PCR and PLS analysis, respectively. The root mean square errors of prediction were found to be 0.00026, 0.0043 and 0.0031 g cm-3, respectively. It is found that near-infrared spectroscopy combined with neural network analysis is useful for the efficient and accurate determination of PE density.
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  • Masahiko SUENAGA
    Type: Technical paper
    2003 Volume 2 Issue 1 Pages 41-48
    Published: 2003
    Released: May 16, 2003
    JOURNALS FREE ACCESS
    A server/client type reagent management system was developed. The system is briefly illustrated in Figure 1. PostgreSQL 6.5.1 running on the RedHat Linux 6.1 serves as a database. As a client to the database server, reagent management software was newly programmed with Java language. In order to obtain the weight readings automatically, an electric balance is connected to the client machine via RS-232C. Additionally, the barcode reader facilitates barcode input.
    In the system, each of the reagents is managed by a barcode labled on the bottle. Since the system is server/client type, multiusers can access the database simultaneously from remote client machines and the maintenance of the database can be centralized.
    The client software including the source code can be downloaded from the Web site of the author.
    http://hb6.seikyou.ne.jp/home/zzzfelis
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