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.

---

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.

     

曲率流的参数化有限元逼近

许多物理现象可以在数学上描述为受曲率驱动的自由界面运动,例如薄膜和泡沫的演变、晶体生长,等等.这些薄膜和界面的运动常依赖于其表面曲率,从而可以用相应的曲率流来描述,其相关自由界面问题的数值计算和误差分析一直是计算数学领域中的难点.参数化有限元法是曲率流的一类有效计算方法,已经能够成功模拟一些曲面在几类基本的曲率流下的演化过程.本文重点讨论曲率流的参数化有限元逼近,它的产生、发展和当前的一些挑战.     

曲边区域上的多边形网格间断有限元离散及其多重网格算法

本文利用多边形网格上的间断有限元方法离散二阶椭圆方程,在曲边区域上,采用多条直短边逼近曲边的以直代曲的策略,实现了高阶元在能量范数下的最优收敛.本文还将这一方法用于带曲边界面问题的求解,同样得到高阶元的最优收敛.此外我们还设计并分析了这一方法的\linebreakW-cycle和Variable V-cycle多重网格预条件方法,证明当光滑次数足够多时,多重网格预条件算法一致收敛.最后给出了数值算例,证实该算法的可行性并验证了理论分析的结果.     

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‐dimensional wave impact on a rigid structure using smoothed particle hydrodynamics

Navier–Stokes computations of a wave–structure interaction are performed with the aim of assessing the potential of smoothed particle hydrodynamics to accurately estimate impact loading time history. A three‐dimensional dam‐break flow with a rectangular column located downstream is considered. The net force and impulse exerted on the column is monitored throughout the simulation with the results correlating well with existing experimental data. Initial and boundary conditions and numerical parameters are varied and their effect on the column load investigated. The column load is found to be most sensitive to the choice of boundary treatment. Copyright © 2011 John Wiley & Sons, Ltd.     

An ALE finite element method for a coupled Stefan problem and Navier–Stokes equations with free capillary surface

In this article, an ALE finite element method to simulate the partial melting of a workpiece of metal is presented. The model includes the heat transport in both the solid and liquid part, fluid flow in the liquid phase by the Navier–Stokes equations, tracking of the melt interface solid/liquid by the Stefan condition, treatment of the capillary boundary accounting for surface tension effects and a radiative boundary condition. We show that an accurate treatment of the moving boundaries is crucial to resolve their respective influences on the flow field and thus on the overall energy transport correctly. This is achieved by a mesh‐moving method, which explicitly tracks the phase boundary and makes it possible to use a sharp interface model without singularities in the boundary conditions at the triple junction. A numerical example describing the welding of a thin‐steel wire end by a laser, where all aforementioned effects have to be taken into account, proves the effectiveness of the approach.Copyright © 2012 John Wiley & Sons, Ltd.     

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