Polynomials of Pellian Type and Continued Fractions

We investigate infinite families of integral quadratic polynomials {fk (X)} k∈N and show that, for a fixed k ∈ N and arbitrary X ∈ N, the period length of the simple continued fraction expansion of √fk (X) is constant. Furthermore, we show that the period lengths of √fk (X) go to infinity with k. For each member of the families involved, we show how to determine, in an easy fashion, the fundamental unit of the underlying quadratic field. We also demonstrate how the simple continued fraction ex- pansion of √fk (X) is related to that of √C, where √fk (X) = ak*X^2 +bk*X + C. This continues work in [1]–[4].

Solving Maximum Clique Problem for Protein Structure Similarity

Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum weighted clique problems in specific k-partite graphs, referred here as alignment graphs. In this paper we present both a new integer programming formulation for solving such clique problems and a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches have been integrated in VAST, a software for aligning protein 3D structures largely used in the National Center for Biotechnology Information, an original clique solver which uses the well known Bron and Kerbosch algorithm (BK). Our computational results on real protein alignment instances show that our branch and bound algorithm is up to 116 times faster than BK.