LIMITING BEHAVIOR OF UNIFORM RECURSIVE TREES

The authors consider the limiting behavior of various branches in a uniform recursive tree with size growing to infinity.The limiting distribution ofζ_(n,m),the number of branches with size m in a uniform recursive tree of order n,converges weakly to a Poisson distribution with parameter 1/m with convergence of all moments.The size of any large branch tends to infinity almost surely.     

Tree-gel and loop-gel conversions in nonlinear polymerization

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Equilibrium polymerization in a solvent: Solution on the Bethe lattice

The lattice model for equilibrium polymerization in a solvent proposed by Wheeler and Pfeuty is solved exactly on a Bethe lattice (core of a Caylay tree) with general coordination numberq. Earlier mean-field results are reobtained in the limitq, but the phase diagrams show deviations from them for finiteq. Whenq=2, our results turn into the solution of the one-dimensional problem. Although the model is solved directly, without the use of the correspondence between the equilibrium polymerization model and the diluten0 model, we verified that the latter model may also be solved on the Bethe lattice, its solution being identical to the direct solution in all parameter space. As observed in earlier studies of the puren0 vector model, the free energy is not always convex. We obtain the region of negative susceptibility for our solution and compare this result with mean field and renormalization group (-expansion) calculations.     

On the Randić Index of Acyclic Conjugated Molecules

The Randić index of an organic molecule whose molecular graph is G is the sum of the weights (d(u)d(v))^−1/2 of all edges uv of G, where d(u) and d(v) are the degrees of the vertices u and v in G. We give a sharp lower bound on the Randić index of conjugated trees (trees with a perfect matching) in terms of the number of vertices. A sharp lower bound on the Randić index of trees with a given size of matching is also given Mei Lu: Partially supported by NNSFC (No. 60172005) Lian-zhu Zhang: Partially supported by NNSFC (No. 10271105) Feng Tian: Partially supported by NNSFC (No. 10431020)     

Fast folding and comparison of RNA secondary structures

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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Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

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.

     

N叉树上的离散时间量子随机行走

通过离散时间量子随机行走的框架,我们研究了在N叉树上的离散时间量子随机行走,该框架不需要硬币空间,仅仅只需要选择一个除了酉性再无其它限制的演化算子,并且包含了使用再生结构的轨道枚举和z变换.作为结果,我们在封闭形式中计算了在根处的振幅的生成函数.     

The least element property of center location on tree networks with applications to distance and precedence constrained problems

In the classicalp-center location model on a network there is a set of customers, and the primary objective is to selectp service centers that will minimize the maximum distance of a customer to a closest center. Suppose that thep centers receive their supplies from an existing central depot on the network, e.g. a warehouse. Thus, a secondary objective is to locate the centers that optimize the primary objective as close as possible to the central depot. We consider tree networks and twop-center models. We show that the set of optimal solutions to the primary objective has a semilattice structure with respect to some natural ordering. Using this property we prove that there is ap-center solution to the primary objective that simultaneously minimizes every secondary objective function which is monotone nondecreasing in the distances of thep centers from the existing central depot.Restricting the location models to a rooted path network (real line) we prove that the above results hold for the respective classicalp-median problems as well.     

A graphical method to construct a phylogenetic tree

A 3D graphical representation of DNA sequences, which has no circuit or degeneracy, is derived for mathematical denotation of DNA sequence. Based on this graphical representation, we propose a new sequence distance measure. We make use of the corresponding similarity matrix to construct a phylogenic tree by virtue of the fuzzy theory. The examination of phylogenic tree belong to eight species illustrates the utility of our approach. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Three‐unit semicircles curve: A compact 3D graphical representation of DNA sequences based on classifications of nucleotides

A new three‐dimensional graphical representation of DNA sequences, three‐unit semicircles (TUS)‐curve, which maps a given sequence into a dot sequences embedded in three‐unit semicircles, is proposed based on three biclassifications of nucleotides. TUS‐curve has the merit of compactness and could avoid the degeneracy and loss of information. The geometrical center of the curve, which indicates the distribution of base frequencies of the corresponding DNA sequence, is extracted and applied to analyze the similarity of various species. Phylogenetic tree of 11 species based on their first exons of β‐globin genes showed that the TUS‐curve is a powerful tool to get valuable biological information. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

On the normalized Laplacian of Möbius phenylene chain and its applications

Let denote a molecular graph of linear [n] phenylene with n hexagons and n squares, and let the Möbius phenylene chain be the graph obtained from the by identifying the opposite lateral edges in reversed way. Utilizing the decomposition theorem of the normalized Laplacian characteristic polynomial, we study the normalized Laplacian spectrum of , which consists of the eigenvalues of two symmetric matrices ℒ _R and ℒ _Q of order 3n. By investigating the relationship between the roots and coefficients of the characteristic polynomials of the two matrices above, we obtain an explicit closed-form formula of the multiplicative degree-Kirchhoff index as well as the number of spanning trees of . Furthermore, we determine the limited value for the quotient of the multiplicative degree-Kirchhoff index and the Gutman index of .