Edge Distance-based Topological Indices of Strength-weighted Graphs and their Application to Coronoid Systems, Carbon Nanocones and SiO2 Nanostructures.

The edge-Wiener index is conceived in analogous to the traditional Wiener index and it is defined as the sum of distances between all pairs of edges of a graph G. In the recent years, it has received considerable attention for determining the variations of its computation. Motivated by the method of computation of the traditional Wiener index based on canonical metric representation, we present the techniques to compute the edge-Wiener and vertex-edge-Wiener indices of G by dissecting the original graph G into smaller strength-weighted quotient graphs with respect to Djokovic-Winkler relation. These techniques have been applied to compute the exact analytic expressions for the edge-Wiener and vertex-edge-Wiener indices of coronoid systems, carbon nanocones and SiO2 nanostructures. In addition, we have reduced these techniques to the subdivision of partial cubes and applied to the circumcoronene series of benzenoid systems.

Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments.

Protein structures evolved through a complex interplay of cooperative interactions, and it is still very challenging to design new protein folds de novo. Here we present a strategy to design self-assembling polypeptide nanostructured polyhedra based on modularization using orthogonal dimerizing segments. We designed and experimentally demonstrated the formation of the tetrahedron that self-assembles from a single polypeptide chain comprising 12 concatenated coiled coil-forming segments separated by flexible peptide hinges. The path of the polypeptide chain is guided by a defined order of segments that traverse each of the six edges of the tetrahedron exactly twice, forming coiled-coil dimers with their corresponding partners. The coincidence of the polypeptide termini in the same vertex is demonstrated by reconstituting a split fluorescent protein in the polypeptide with the correct tetrahedral topology. Polypeptides with a deleted or scrambled segment order fail to self-assemble correctly. This design platform provides a foundation for constructing new topological polypeptide folds based on the set of orthogonal interacting polypeptide segments.

Omega polynomial revisited.

Omega polynomial was proposed by Diudea (Omega Polynomial, Carpath. J. Math., 2006, 22, 43-47) to count the opposite topologically parallel edges in graphs, particularly to describe the polyhedral nanostructures. In this paper, the main definitions are re-analyzed and clear relations with other three related polynomials are established. These relations are supported by close formulas and appropriate examples.

Three methods for calculation of the hyper-Wiener index of molecular graphs.

The hyper-Wiener index WW of a graph G is defined as WW(G) = (summation operator d (u, v)(2) + summation operator d (u, v))/2, where d (u, v) denotes the distance between the vertices u and v in the graph G and the summations run over all (unordered) pairs of vertices of G. We consider three different methods for calculating the hyper-Wiener index of molecular graphs: the cut method, the method of Hosoya polynomials, and the interpolation method. Along the way we obtain new closed-form expressions for the WW of linear phenylenes, cyclic phenylenes, poly(azulenes), and several families of periodic hexagonal chains. We also verify some previously known (but not mathematically proved) formulas.