Parameters as an index to efficiently assess the pollution level of the upper, middle, and lower streams of the Tamagawa (Tokyo, Japan) based on measured water quality were determined by using multivariate analysis, principal component analysis (PCA), and cluster analysis (CA) for data measured from 1994 to 2002. Missing data during 2000-2002 were estimated using a perceptron type neural network and arithmetic progression. The combination of scores for the first and second principal components obtained by PCA enabled classification of the upper, middle, and lower streams of the Tamagawa. The CA results corresponded well with the PCA results. Based on the score of the first principal compornent determined here, contributions to the water pollution of the middle and lower streams should be decreased to improve the water quality of the Tamagawa.
Computational analysis of minor and major groove methidium-DNA complexes in B-form DNA 5'-d(CATCCCGGGATG) is performed for intercalation at each base pair. The most stable structure based on stabilization energies was calculated by a combination of molecular mechanics (augmented MM2) and molecular dynamics (MD) methods. When methidium intercalates from the minor groove, the phenanthridine ring is parallel to the nucleobase pairs, and the excluded site size is 6.4 Å. The stabilization is maximal when the methidium intercalates between 5'-d(CG) from the minor groove (-28.3 kcal·mol-1). Calculations using MD showed that the complex was considerably less stable when the methidium intercalated from the major groove. This result is consistent with experimental results demonstrating that the intercalation of methidium occurs from the minor groove. A plot of the calculated stabilization energy vs. the logarithm of the binding constant of ethidium bromide with each dinucleotide affords a linear relationship.
Monosubstituted alkanes as stereoisomers, not as constitutional isomers, are regarded as planted three-dimensional (3D) trees, which are defined as a 3D extension of planted trees (graphs). They are thus recognized as 3D-objects (planted promolecules) and enumerated by Fujita's proligand method (Fujita S (2005) Theor. Chem. Acc. 113:73–79, 113:80–86, Fujita S (2006) Theor. Chem. Acc. 115:37–53). By starting from three kinds of sphericity indices, i.e., ad for homospheric cycles, cd for enantiospheric cycles, and bd for hemispheric cycles, cycle indices with chirality fittingness (CI-CFs) are obtained to enumerate planted 3D-trees or equivalently monosubstituted alkanes as stereoisomers. Functional equations a(x), c(x2), and b(x) for recursive calculations are derived from the CI-CFs and programmed in three ways by means of the Maple programming language. The three recursive procedures for calculating the numbers of planted 3D-trees are executed to give identical results, which are collected up to 100 carbon content in a tabular form. The results are compared with the enumeration of planted trees (as graphs).
Monosubstituted alkanes are counted as stereoisomers by means of Fujita's proligand method (Fujita S (2005) Theor. Chem. Acc. 113:73-79, 113:80-86, Fujita S (2006) Theor. Chem. Acc. 115:37-53), where the numbers of primary, secondary, and tertiary ones are calculated after deriving respective functional equations. The procedures of counting are programmed by means of the Maple programming language. They are executed and the results collected up to carbon content 100 in a tabular form. By omitting the sphericities of the recursive functions a(x), c(x2), and b(x) so as to give a single dummy variable r(x), such functional equations with sphericity are transformed into Pólya's functional equations without sphericity, which are applied to the enumeration of primary, secondary, and tertiary monosubstituted alkanes as graphs (chemically, constitutional isomers). The results of Fujita's proligand method are compared with those based on Pólya's theorem in connection with several cases of pseudoasymmetry.