Analysis of RNA sequence structure maps by exhaustive enumeration I. Neutral networks

Summary Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of allGC andAU sequences with chain lengths up to 30. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based on statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them that ofneutral networks (being sets of sequences folding into the same structure). Exhaustive enumeration allows to test several previously suggested relations: the number of (minimum free energy) secondary structures as a function of the chain length as well as the frequency distribution of structures at constant chain length (commonly resulting in generalized forms ofZipf's law).

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Analyse der Beziehungen zwischen RNA-Sequenzen und Sekundärstrukturen durch vollständige Faltung, 1. Mitt. Faltung, Neutrale Netzwerke

Zusammenfassung Die globalen Benziehungen zwischen RNA-Sequenzen und Sekundärstrukturen werden als Abbildungen aus einem Raum aller Sequenzen in einen Raum aller Strukturen aufgefaßt. Diese Abbildungen werden durch Falten aller binären Sequenzen desGC-undAU-Alphabets mit Kettenlängen bis zun=30 untersucht. Die berechneten Strukturdaten werden durch vollständiges Abzählen ausgewertet und als eine exakte Referenz zum Überprüfen analytischer Resultate aus mathematischen Modellen sowie zum Testen statistisch erhobener Proben verwendet. Einige neuartige Konzepte zur Beschreibung der Beziehungen zwischen Sequenzen und Strukturen werden eingehend untersucht, unter ihnen der Begriff derneutralen Netzwerke. Ein neutrales Netzwerk besteht aus allen Sequenzen, die eine bestimmte Struktur ausbilden. Vollständiges Abzählen ermöglicht beispielsweise die Bestimmung aller Strukturen minimaler freier Energie in Abhängigkeit von der Kettenlänge ebenso wie die Bestimmung der Häufigkeitsverteilungen der Strukturen bei konstanten Kettenlängen. Die letzteren folgen einer verallgemeinerten FormZipfschen Gesetzes.

     

Gem-dinitro compounds in organic synthesis. 4. Use of the condensation product of glyoxal and dinitromethane in the synthesis of nitro-1,2,3-triazoles

The condensation of dinitromethane with glyoxal has been investigated and it has been demonstrated that 1,1,4,4-tetranitro-2,3-butandiol, -hydroxy-,-dinitropropionic acid or their mixture may be formed. Interaction of 1,1,4,4-tetranitro-2,3-butandiol or 1,4-dibromo-1,1,4,4-tetranitro-2,3-butanediol diacetates with sodium azide leads to bis(5-nitro-1,2,3-triazol-4-yl) via intermediate 1,1,4,4-tetranitro-1,3-butadiene.For communication 3, see [1].N. D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences, 117913 Moscow. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 9, pp. 2123–2131, September, 1992.     

A greedy algorithm for finding maximum spanning trees in infinite graphs

In finite graphs, greedy algorithms are used to find minimum spanning trees (MinST) and maximum spanning trees (MaxST). In infinite graphs, we illustrate a general class of problems where a greedy approach discovers a MaxST while a MinST may be unreachable. Our algorithm is a natural extension of Prim's to infinite graphs with summable and strictly positive edge weights, producing a sequence of finite trees that converge to a MaxST.     

Large cycles in random generalized Johnson graphs

This paper studies thresholds in random generalized Johnson graphs for containing large cycles, i.e. cycles of variable length growing with the size of the graph. Thresholds are obtained for different growth rates.     

Spectra of graphs and fractal dimensions II

This paper continues the study of exponentsd(x), d (x), d _R (x) andd (x) for graphG; and the nearest neighbor random walk {X _n } _nN onG, if the starting pointX ₀=x is fixed. These exponents are responsible for the geometric, resistance, diffusion and spectral properties of the graph. The main concern of this paper is the relation of these exponents to the spectral density of the transition matrix. A series of new exponentse, e ,e _R ,e are introduced by allowingx to vary along the vertices. The results suggest that the geometric and resistance properties of the graph are responsible for the diffusion speed on the graph.     

Covering with blocks in the non-symmetric case

Considering an infinite string of i.i.d. random letters drawn from a finite alphabet we define the cover timeW _n as the number of random letters needed until each pattern of lenghtn appears at least once as a substring. Sharp weak and a.s. limit results onW _n are known in the symmetric case, i.e., when the random letters are uniformly distributed over the alphabet. In this paper we determine the limit distribution ofW _n in the nonsymmetric case asn. Generalizations in terms of point processes are also proved.Dedicated to Endre Csáki on his 60th birthday.