Approximating the maximum 2- and 3-edge-colorable subgraph problems

For a fixed value of a parameter k≥2, the Maximum k-Edge-Colorable Subgraph Problem consists in finding k edge-disjoint matchings in a simple graph, with the goal of maximising the total number of edges used. The problem is known to be -hard for all k, but there exist polynomial time approximation algorithms with approximation ratios tending to 1 as k tends to infinity. Herein we propose improved approximation algorithms for the cases of k=2 and k=3, having approximation ratios of 5/6 and 4/5, respectively.     

On the complexity of some subgraph problems

We study the complexity of the problem of deciding the existence of a spanning subgraph of a given graph, and of that of finding a maximum (weight) such subgraph. We establish some general relations between these problems, and we use these relations to obtain new NP-completeness results for maximum (weight) spanning subgraph problems from analogous results for existence problems and from results in extremal graph theory. On the positive side, we provide a decomposition method for the maximum (weight) spanning chordal subgraph problem that can be used, e.g., to obtain a linear (or O(nlogn)) time algorithm for such problems in graphs with vertex degree bounded by 3.     

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.

     

Closed‐form formulas for Kirchhoff index

We find closed‐form expressions for the resistance, or Kirchhoff index, of certain connected graphs using Foster's theorems, random walks, and the superposition principle. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 135–140, 2001     

An Improved Plotting Package Applied to Chemical Graphing Problems

Abstract

A plotting package, written in LINC assembly language, is described. It produces high quality graphs and labels the graphs for direct submission to professional journals. A μ-LINC (Laboratory INstrument (Computer) is used to compute least-squares fitted curves and lines from data entered either on-or off-line and to draw the graphs directly on an incremental plotter. Bar graphs, line graphs, and fitted data can be plotted with options to suppress the lines and/or the points.     

Complete graph conjecture for inner-core electrons: homogeneous index case

The complete graph conjecture that encodes the inner-core electrons of atoms with principal quantum number n >or= 2 with complete graphs, and especially with odd complete graphs, is discussed. This conjecture is used to derive new values for the molecular connectivity and pseudoconnectivity basis indices of hydrogen-suppressed chemical pseudographs. For atoms with n = 2 the new values derived with this conjecture are coincident with the old ones. The modeling ability of the new homogeneous basis indices, and of the higher-order terms, is tested and compared with previous modeling studies, which are centered on basis indices that are either based on quantum concepts or partially based on this new conjecture for the inner-core electrons. Two similar algorithms have been proposed with this conjecture, and they parallel the two "quantum" algorithms put forward by molecular connectivity for atoms with n > 2. Nine properties of five classes of compounds have been tested: the molecular polarizabilities of a class of organic compounds, the dipole moment, molar refraction, boiling points, ionization energies, and parachor of a series of halomethanes, the lattice enthalpy of metal halides, the rates of hydrogen abstraction of chlorofluorocarbons, and the pED(50) of phenylalkylamines. The two tested algorithms based on the odd complete graph conjecture give rise to a highly interesting model of the nine properties, and three of them can even be modeled by the same set of basis indices. Interesting is the role of some basis indices all along the model.     

Asymptotically independent topological indices on random trees

Topological indices are graph invariants used in computational chemistry to encode molecules. A frequent problem when performing structure-activity studies is that topological indices are inter-correlated. We consider a simple topological index and show asymptotic independence for a random tree model. This continues previous work on the correlation among topological indices. These findings suggest that a size-dependence in a certain class of distance-based topological indices can be eliminated.AMS subject classification: 05C80, 60E10, 92E10     

Graph theoretical procedure for obtaining analytical expressions of eigenspectra of linear chains and cycles with alternant vertex weights and same edge weight: Application to some complicated graphs

A graph theoretical procedure for obtaining eigenvalues of linear chains and cycles having alternant vertex weights (h₁, h₂, h₁, h₂, h₁, h₂, …) and the same edge weight (k) have been developed. The eigenvalues of some complicated graphs, such as graphs of linear polyacenes, methylene‐substituted linear polyacenes and cylindrical polyacene strips, stack graphs, and reciprocal graphs have been shown to be generated in closed analytical forms by this procedure. Many such graphs represent chemically important molecules or radicals. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Interconnection networks for parallel molecular dynamics simulation based on hamiltonian cubic symmetric topology

A class of interconnection networks for efficient parallel MD simulations based on hamiltonian cubic symmetric graphs is presented. The cubic symmetric graphs have many desirable properties as interconnection networks since they have a low degree and are vertex- and edge-transitive. We present a method for scheduling collective communication routines that are used in parallel MD and are based on the property that the graphs in question have a Hamilton cycle, that is, a cycle going through all vertices of the graph. Analyzing these communication routines shows that hamiltonian cubic symmetric graphs of small diameter are good candidates for a topology that gives rise to an interconnection network with excellent properties, allowing faster communication and thus speeding up parallel MD simulation.