title: A P system and a constructive membrane-inspired DNA algorithm for solving the Maximum Clique Problem.
abstract: We present a P system with replicated rewriting to solve the Maximum Clique Problem for a graph. Strings representing cliques are built gradually. This involves the use of inhibitors that control the space of all generated solutions to the problem. Calculating the maximum clique for a graph is a highly relevant issue not only on purely computational grounds, but also because of its relationship to fundamental problems in genomics. We propose to implement the designed P system by means of a DNA algorithm. This algorithm is then compared with two standard papers that addressed the same problem and its DNA implementation in the past. This comparison is carried out on the basis of a series of computational and physical parameters. Our solution features a significantly lower cost in terms of time, the number and size of strands, as well as the simplicity of the biological implementation.
authors.affiliation: Departamento Inteligencia Artificial, Universidad Politécnica de Madrid (UPM), Boadilla del Monte s/n, 28660 Madrid, Spain. mgarciaarnau@alumnos.upm.es
authors.forename: Marc
authors.initials: M
authors.lastname: García-Arnau
authors.forename: Daniel
authors.initials: D
authors.lastname: Manrique
authors.forename: Alfonso
authors.initials: A
authors.lastname: Rodríguez-Patón
authors.forename: Petr
authors.initials: P
authors.lastname: Sosík
mesh_terms: D000465:Algorithms; D039301:Computers, Molecular; D008433:Mathematics; D049490:Systems Biology