Journal of Chemical Software
Online ISSN : 1883-8359
Print ISSN : 0918-0761
Volume 5 , Issue 1
Showing 1-4 articles out of 4 articles from the selected issue
  • Yuichiro KIRIYAMA, Hisao SUZUKI, Shigeko OZAKI, Takayuki YANO, Nozomu ...
    1999 Volume 5 Issue 1 Pages 1-14
    Published: March 15, 1999
    Released: March 28, 2000
    JOURNALS FREE ACCESS
    We have equipped a teaching aid system with interactive teaching materials using Java. These materials are provided on a World Wide Web (WWW) client server system, and they will stimulate positive participation of students in the course of study for various clients. These materials have attractive features, such as easily manageable human interface and virtual reality. The teaching aid system can give students not only knowledge about natural sciences but also a way of choosing among associated items for study according to their achievement and/or interest. The system has been designed so as to complement a supplementary lecture for backward students in our university. As a matter of course, identification of students and their access records are automatically carried out. A communication channel between students and teachers is also provided. In these points, the system is sufficiently suitable for supplementary education for science lectures in a non-science oriented university. As a result, it may lighten the extra burden imposed on teachers. Some teaching materials are open to the public (http://sciwww.misc.hit-u.ac.jp:8888/).
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  • Fumio NOGUCHI, Nobuki HANAOKA, Yasuhisa URANO, Hidehiko KOBAYASHI, Hir ...
    1999 Volume 5 Issue 1 Pages 15-28
    Published: March 15, 1999
    Released: March 28, 2000
    JOURNALS FREE ACCESS
    Many PC applications which can visualize various crystal structures have developed as PC ability has enhanced year by year. But workers engaging in design of materials are eager to know vacant space sites in crystal structures. However, PC applications can not usually display digital coordinates of vacant spaces because information about vacant spaces is not on memory. We developed the MS-Windows95/MS-WindowsNT application which can display locations and sizes of vacant spaces by scanning all space in a unit cell using infinitesimal change of the calculation position. Arrangement of vacant spaces can be displayed by the 3D graphics of high quality because the application can save a VRML text file(Figure. 5). The user can recognize the stretch of vacant spaces by the cross section drawn by color tones which depend on the sizes of vacant spaces(Figure. 8). In order to use the crystal database of own making, the application was developed by using the Borland C++ builder compiler which includes the database engine. Therefore, the above-mentioned calculations can be easily performed on ca. 3,500 crystals. Furthermore, the user can append new crystal data to the crystal database(Figure. 10). In an inspection of calculated results for spinel, outputs of vacant spaces of maximum size coincided with Wyckoff notation 16c sites belonging to the space group Fd3m(Table 2). It was considered that the calculation of vacant spaces was carried out correctly.
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  • Ayumu SAITO, Koichi NISHIGAKI
    1999 Volume 5 Issue 1 Pages 29-38
    Published: March 15, 1999
    Released: March 28, 2000
    JOURNALS FREE ACCESS
    In order to quantitatively comprehend the essence of whole genome shotgun sequencing, a Monte-Carlo simulation was carried out. It was estimated that even a vast genome such as human genome can be sequenced at a moderate redundancy (∼7) with a satisfactory accuracy (10-4 error rate), resulting in a high sequencing speed and much lower cost. Switching from a random process (i.e., shotgun) to a directed process such as PCR-relay was shown to be ultimately important for a whole genome shotgun sequencing not to inflate its cost. An equation to evaluate the optimum switching point was introduced as a function of coverage, which also depends on the costs of a shotgun process and a directed one for sequencing a unit length. Moderate redundancy was underscored to have more merits in speed and accuracy than its demerit of being redundant. Our simulation for estimating redundancy was basically consistent with the results of the current whole genome shotgun sequencing. As a conclusion, whole genome shotgun sequencing applied to a vast genome is estimated to be effective.
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  • Takeshi UNO, Haruhisa HAYASHI, Kazushige YAMANA, Hidehiko NAKANO
    1999 Volume 5 Issue 1 Pages 39-48
    Published: March 05, 1999
    Released: March 28, 2000
    JOURNALS FREE ACCESS
    A support program for AMBER was developed on the basis of the biomolecular graphics program “Modrast-P". This program has three features, which are : 1) Setting up of input files for AMBER. It is easy and efficient to make input files for AMBER modules (Figure 1) by using interactive and graphical operations. 2) Molecular modeling for building the initial structure of the molecule for molecular dynamics calculation by use of the extended function of Modrast-P. 3) Animations of atomic trajectory files from molecular dynamics simulations, calculations of atom-to-atom distances and the extraction of potential energies from output files in order to draw graphs for getting quantitative information, are possible.As an example use of this program, the structure of DNA containing anthraquinone groups was simulated (Figures 2,3).This program runs on any UNIX workstations and personal computers where PC-UNIX, such as Linux, are installed.
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