Journal of Chemical Software
Online ISSN : 1883-8359
Print ISSN : 0918-0761
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Volume 3 , Issue 3
Showing 1-4 articles out of 4 articles from the selected issue
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  • Shin-ichi NAKAYAMA, Masayuki YOSHIDA
    Volume 3 (1996 - 1997) Issue 3 Pages 97-108
    Released: August 13, 2009
    JOURNALS FREE ACCESS
    The comparison algorithm of protein sequences by Murata was modified by considering only similarities between the same amino acid types and by introducing a lookup table. The modified algorithm calculates the similarity score between two protein sequences and aligns them. Computational times for calculating similarity scores against some proteins to all proteins in the Protein Sequence Database of the PIR by the system implementing our algorithm are about ten times shorter than those achieved by Murata. The alignments by our algorithm with a gap penalty of 18 are similar to those by Murata. The computational times by our system are two to three times slower, but the similarity scores are more sensitive than those by FASTA.
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  • Yuji SHINOHARA, Tsuyoshi NAKAJIMA, Shozi MISHIMA
    Volume 3 (1996 - 1997) Issue 3 Pages 109-120
    Released: February 09, 2010
    JOURNALS FREE ACCESS
    A computer program was prepared to calculate time-courses of concentrations of chemical species involved in a chemical reaction. On the basis of Runge-Kutta iteration method, the program integrates numerically simultaneous differential equations which express relations between the concentrations and the rates of these changes. The program was designed to monitor the rates for all species from moment to moment, to select the best-suited iteration interval for the integration and then to carry out the integration with the interval. The program was applied to the following reaction systems : 1) oscillatory reaction in an aqueous solution of IO3-, H+, I2, I-and H2O2; 2) saponification of ethyl acetate; and 3) gas phase chain reaction of bromine with hydrogen. The results showed that the program gave accurate time-courses of the concentrations of reactants and products in relatively short processing time.
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  • Teruo YOSHINO
    Volume 3 (1996 - 1997) Issue 3 Pages 121-128
    Released: February 09, 2010
    JOURNALS FREE ACCESS
    13C-NMR database of sugars is made on Macintosh computer by using a database software, File Maker pro developed by Claris Co. This database is a sister of 1H-NMR database which has been reported by the author and can be referred to on the same display by combining data of a specified sample using the look-up function of File Maker pro. This utility may be useful for the individual carbohydrate chemist to make spectral identification of sugars of unknown structure. In addition, this database has several useful functions;output data on screen or printer with several layouts such as data-card in which NMR data are combined with chemical structure, data-table with results of statistics calculations, etc.
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  • Hisashi MIYATA, Yoshio TODA, Takashi OHNO
    Volume 3 (1996 - 1997) Issue 3 Pages 129-138
    Released: August 13, 2009
    JOURNALS FREE ACCESS
    A new approach to three dimensional cluster has been devised as an extension of the diffusion-limited aggregation (DLA) model. A graphics simulation shows that clusters formed are composed mainly of ca. 10 particles. The interaction force between particles and the cluster anisotropy does not affect cluster size significantly. From the results the effects of three dimensional DLA, cluster anisotropy and the interaction with the fractal dimension have been discussed.
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