{"title":"A Program for Numerical Integration of Reaction Rate Laws on the Basis of the Runge-Kutta Method","authors":"Yuji Shinohara, T. Nakajima, S. Mishima","doi":"10.2477/JCHEMSOFT.3.109","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.3.109","url":null,"abstract":"化学反応における化学種の濃度の時間変化を求めるために、反応速度式をRunge-Kutta法を用いて数値積分するプログラムを作成した。数値積分に際しては、反応に含まれる化学種の濃度の時間変化の大きさをチェックし、それに応じて積分間隔を適当に選択する手法を採用した。本プログラムを1) IO3-, H+, I2, I-, H2O2を含む溶液の振動反応、2) エステルのけん化反応、および3) 水素―臭素反応の3種類の反応に適用した。その結果、本プログラムを使用することによって、濃度の時間変化が比較的短時間で計算できることが確認された。","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1996-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129104111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"Comparison Algorithm of Protein Sequences by Introducing a Lookup Table","authors":"Shin-ichi Nakayama, Masayuki Yoshida","doi":"10.2477/JCHEMSOFT.3.97","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.3.97","url":null,"abstract":"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.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1996-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115339092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Simulations of Aggregation Processes of Cluster by Extended Diffusion-Limited Model (2) -Fractal Dimension of three Dimensional Cluster","authors":"H. Miyata, Y. Toda, T. Ohno","doi":"10.2477/JCHEMSOFT.3.129","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.3.129","url":null,"abstract":"基盤上に固定されるクラスターの生成過程の拡張DLA (Diffusion-Limited Aggregation) によるモデルを提案した.拡散律速下でのクラスター成長過程を3次元クラスターの生成に拡張し, 異方性や粒子間引力の影響を考慮した新しいモデルを考案した.クラスターの形状の視覚化を試み, フラクタル次元によるクラスターの形状解析を検討した.被覆率が15%以内で, 引力の有効距離が0～2の間では, 10個程度の粒子が凝集したクラスターが形成されることがわかった.このときのフラクタル次元は1.0～1.2と一定で, r/p比や引力項によってそれほど変化しない.これは, フラクタル図形であることを示している.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1996-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124237014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
5種類のPAH (ベンゾ[a]ピレン、ペリレン、フルオランテン、ピレン、およびクリセン) の濃度を10-2～10-1μgcm-3の範囲で種々変化させたn―ヘキサン溶液の蛍光スペクトル (Ex : 305nm, Em : 330～520nm) をアスキー形式のデータセットに変換した後マイクロコンピュータに読み込みPLS (Partial Least Squares) 回帰分析法を用いて回帰モデルを構築した。別に作成した濃度既知の合成試料溶液の蛍光スペクトルに回帰モデルを適用し、5種類のPAHについて計算して得られた予測値と良い一致を見た。
在10-2 ~ 10-1μgcm-3的范围内，使5种PAH(苯并[a]芘、培利烯、氟烯、芘和丝线)的浓度发生各种变化的n -己烷溶液的荧光光谱(Ex:305nm, Em:将330 ~ 520nm)转换为asski形式的数据集，然后读取到微型计算机中，使用PLS (Partial Least Squares)回归分析法建立回归模型。将回归模型应用于另制作的已知浓度合成样品溶液的荧光光谱，与计算5种PAH得到的预测值一致。
{"title":"Simultaneous Fluorometric Determination of Polycyclic Aromatic Hydrocarbons by Multivariate Regression Analysis","authors":"S. Yamaguchi, T. Kumagai, H. Nishioka","doi":"10.2477/JCHEMSOFT.3.65","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.3.65","url":null,"abstract":"5種類のPAH (ベンゾ[a]ピレン、ペリレン、フルオランテン、ピレン、およびクリセン) の濃度を10-2～10-1μgcm-3の範囲で種々変化させたn―ヘキサン溶液の蛍光スペクトル (Ex : 305nm, Em : 330～520nm) をアスキー形式のデータセットに変換した後マイクロコンピュータに読み込みPLS (Partial Least Squares) 回帰分析法を用いて回帰モデルを構築した。別に作成した濃度既知の合成試料溶液の蛍光スペクトルに回帰モデルを適用し、5種類のPAHについて計算して得られた予測値と良い一致を見た。","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1996-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130484705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Surface Energy Calculation of Face Centered Cubic Lattice Metals","authors":"Yasuhisa Urano, F. Noguchi, H. Miura","doi":"10.2477/JCHEMSOFT.3.91","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.3.91","url":null,"abstract":"パソコンを用いて、面心立方格子金属の各種結晶面の挿入原子法による表面エネルギーの計算を行い、文献値と比較した。また、金及び白金の (110) 2×1再構成表面の計算において、今回用いた挿入原子法のパラメータで、エネルギー的に安定になることを確認した。","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1996-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134368138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tadayosi Yoshimura, Yoshihiro Aoyama, Hiroshi Ohtake, Yasuaki Sasamura, J. Shimozawa, B. T. Newbold
There are many software in the field of chemical education. However, it was found, via student questionnaires, that these software have some defects, for example students like to see more realistic graphics rather than the computer graphics, and teachers also like to have a more intractive approach in their classes. We have developed new type CAI software to solve these difficulties by using a new technique which enables us to use different multimedia sources as part of original CAI programs.These multimedia software will hopefully improve the use of CAI programs in chemical education. In particular, we edited the video movie into a short interval (a few minutes) file and used it in CAI programs as an original and novel method.
{"title":"Development of Software for Chemical Education Using Multimedia Techniques","authors":"Tadayosi Yoshimura, Yoshihiro Aoyama, Hiroshi Ohtake, Yasuaki Sasamura, J. Shimozawa, B. T. Newbold","doi":"10.2477/JCHEMSOFT.3.73","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.3.73","url":null,"abstract":"There are many software in the field of chemical education. However, it was found, via student questionnaires, that these software have some defects, for example students like to see more realistic graphics rather than the computer graphics, and teachers also like to have a more intractive approach in their classes. We have developed new type CAI software to solve these difficulties by using a new technique which enables us to use different multimedia sources as part of original CAI programs.These multimedia software will hopefully improve the use of CAI programs in chemical education. In particular, we edited the video movie into a short interval (a few minutes) file and used it in CAI programs as an original and novel method.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1996-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125773970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Electronic State of Anthra[1, 9-bc:4, 10-b'c']dichromene and Structural Analysis of Its Endoperoxide","authors":"Tomohiro Watanabe, T. Tachikawa, Nobutaka Kitahara, S. Tokita","doi":"10.2477/JCHEMSOFT.3.59","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.3.59","url":null,"abstract":"芳香族化合物への一重項酸素の付加反応は, ホトクロミックへの応用から極めて興味深い. しかし, 化合物によっては酸素の付加位置を特定することは難しい.アントラ[1,9-b,c:4,10-b';c]ジクロメン (1) の酸素付加体の単結晶を作成し, X線結晶構造解析によって酸素の付加位置を特定した.その結果は, AM1とPM3法によるHOMOの係数からの予測とも一致した.","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1996-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132915992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Crystal Structures of Lipids by the Intermolecular Energy Calculation","authors":"Y. Nakata, T. Takizawa, S. Yabuki, M. Hirai","doi":"10.2477/JCHEMSOFT.3.29","DOIUrl":"https://doi.org/10.2477/JCHEMSOFT.3.29","url":null,"abstract":"","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"26 13","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1996-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131624613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Development of A File Conversion Program for Chemical Structure Data : MOLCONV","authors":"K. Hayami","doi":"10.2477/jchemsoft.3.11","DOIUrl":"https://doi.org/10.2477/jchemsoft.3.11","url":null,"abstract":"","PeriodicalId":205210,"journal":{"name":"Journal of Chemical Software","volume":"97 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1996-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122151978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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