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  • Springer  (6)
  • 1990-1994  (2)
  • 1975-1979  (1)
  • 1970-1974  (3)
  • 1
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract The paper presents a qualitative analysis of the following systems ofn differential equations: $$\dot x_i = x_i x_j - x_i \sum\nolimits_r^n { = 1} x_r x_s {\mathbf{ }}(j = i - 1 + n\delta _{i1} {\mathbf{ }}and{\mathbf{ }}s = r - 1 + n\delta _{r1} )$$ , which show cyclic symmetry. These dynamical systems are of particular interest in the theory of selforganization and biological evolution as well as for application to other fields.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1432-2234
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Zusammenfassung Hydrate der Ionen Li+, Na+, Be2+, F− und Cl− mit den Koordinationszahlen 1, 2, 4, 6 und 8 sowie bis zu drei Hydrathüllen wurden mit Hilfe des CNDO/2-Verfahren berechnet. Die Stärke der Wasserstoffbrücken in den äußeren Sphären wird durch die Ladungsübertragung vom Zentralion zu den Liganden stark beeinflußt. Bei F− unterscheidet sich die mittlere Bindungsenergie in der dritten Sphäre kaum mehr vom reinen Wasser; bei Li+ reicht der Einfluß um eine Wasserhülle weiter. Für beide Ionen wird 6 als günstigste Koordinationszahl erhalten.
    Abstract: Résumé Calcul par la méthode CNDO/2 des hydrates des ions Li+, Na+, Be2+, F− et Cl−, à nombres de coordinence 1, 2, 4, 6 et 8, avec jusqu'à trois couches de molécules d'eau. La force de la liaison hydrogène dans les couches externes est largement déterminée par le transfert de charge à partir de l'ion central vers les ligands. Dans la troisième couche d'hydratation de l'ion F− l'énergie de liaison moeyenne est presque la meme que dans les essaims d'eau pure. Dans le cas de Li+ l'influence de l'ion atteint une couche supplémentaire. Pour ces deux ions le nombre de coordinence 6 s'avère le plus favorable.
    Notes: Abstract Hydrates of the ions Li+, Na+, Be2+, F− and Cl− with coordination numbers 1, 2, 4, 6 and 8 and up to three shells of water molecules were calculated with the CNDO/2 method. The strength of the hydrogen bond in the outer shells is determined largely by the charge transfer from the central ion to the ligands. In the third hydration shell of the F− ion the average binding energy is almost the same as in pure water clusters. In the case of Li+ the influence of the ion reaches one shell further. For both ions the coordination number 6 is the most favourable one.
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  • 3
    ISSN: 1432-1017
    Keywords: Fitness landscapes ; Partition function ; Quasispecies ; RNA secondary structures
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Statistical properties of RNA folding landscapes obtained by the partition function algorithm (McCaskill 1990) are investigated in detail. The pair correlation of free energies as a function of the Hamming distance is used as a measure for the ruggedness of the landscape. The calculation of the partition function contains information about the entire ensemble of secondary structures as a function of temperature and opens the door to all quantities of thermodynamic interest, in contrast with the conventional minimal free energy approach. A metric distance of structure ensembles is introduced and pair correlations at the level of the structures themselves are computed. Just as with landscapes based on most stable secondary structure prediction, the landscapes defined on the full biophysical GCAU alphabet are much smoother than the landscapes restricted to pure GC sequences and the correlation lengths are almost constant fractions of the chain lengths. Correlation functions for multi-structure landscapes exhibit an increased correlation length, especially near the melting temperature. However, the main effect on evolution is rather an effective increase in sampling for finite populations where each sequence explores multiple structures.
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  • 4
    ISSN: 1434-4475
    Keywords: Inverse folding ; parallel computing ; public domain software ; RNA folding ; RNA secondary structures ; tree editing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung. Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung. Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.
    Notes: Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities. An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment. All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.
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  • 5
    ISSN: 1434-4475
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Zusammenfassung Die Umsetzungen von Isobutylidenmeldrumsäure bzw. von 3-Methyl-2-äthoxycarbonylbutyliden-1-meldrumsäure mit Diazoessigester folgen Geschwindigkietsgesetzen 2. Ordnung. Aus der Temperaturabhängigkeit der Reaktionsgeschwindigkeitskonstanten errechnen sich Aktivierungsparameter, die jenen der 1,3-dipolaren Cycloaddition entsprechen. Diese Werte ändern sich nur wenig bei Übergang zu Lösungsmitteln unterschiedlicher Polarität. Die Ergebnisse lassen auf thermisch labile 1-Pyrazoline als Zwischenprodukte schließen, die dann zu den bekannten, stickstoffreien, stabilen Reaktionsprodukten zerfallen.
    Notes: Abstract The reaction of either isobutylidenmeldrum acid or 3-methyl-2-ethoxycarbonylbutyliden-1-Meldrum acid with ethyl diazoacetate exhibits second order kinetics. The values of the activation parameters, calculated from the temperature dependence of the rate constants, correspond to those obtained from 1,3 dipolar cyclo-addition reactions. These values are altered only slightly when the polarity of the solvent is changed. These results suggest that the reaction proceeds via a thermally labile 1-pyrazoline which then decomposes to give nitrogen and the observed products.
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  • 6
    ISSN: 1434-4475
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Zusammenfassung Die Energien und Dipolmomente mehrerer Konformationen von 2,2-Dimethyl-1,3-dioxan-4,6-dion (Meldrumsäure) wurden mit Hilfe der semiempirischenLCAO-MO-SCF-Methode vonPople berechnet. Die Ergebnisse werden mit den experimentellen Dipolmomenten einiger Derivate von 1,3-Dioxan-4,6-dion verglichen. Die Unterschiede zwischen den experimentellen Dipolmomenten dieser Verbindungen können durch Annahme unterschiedlicher Konformerengleichgewichte erklärt werden. Die berechnete Protonenaffinität desMeldrumsäureanions läßt sich in eine Reihe von Aciditäten verschiedenartiger Säuren in Übereinstimmung mit den experimentellen Werten einordnen.
    Notes: Abstract The total energies and dipole moments of some conformations of 2.2-dimethyl-1,3-dioxane-4,6-dione (Meldrum's acid) were calculated withPople's semiempiricalLCAO-MO-SCF-procedure (CNDO). The results are compared with the experimental dipole moments of 2.2-dimethyl-1.3-dioxane-4.6-dione and its alkyl derivatives. The unusual high differences in the experimental dipole moments of this series of compounds are explained by the assumption of different conformational equilibria. The proton affinity ofMeldrum's acid anion fits well into a series of calculated proton affinities of otherBrønsted acids.
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