We are considering sequential membrane systems and molecular dynamics from the viewpoint of Markov chain theory. The configuration space of these systems (including the transitions) is a special kind of directed graph, called a pseudo-lattice digraph, which is closely related to the stoichiometric matrix. Taking advantage of the monoidal structure of this space, we introduce the algebraic notion of precycle. A precycle leads to the identification of cycles by means of the concept of defect, which is a set of geometric constraints on configuration space. Two efficient algorithms for evaluating precycles and defects are given: one is an algorithm due to Contejean and Devie, the other is a novel branch-and-bound tree search procedure. Cycles partition configuration space into equivalence classes, called the communicating classes. The structure of the communicating classes in the free regime–where all rules are enabled–is analyzed: testing for communication can be done efficiently. We show how to apply these ideas to a biological regulatory system.
Cycles and communicating classes in membrane systems and molecular dynamics / M. Muskulus, D. Besozzi, R. Brijder, P. Cazzaniga, S. Houweling, D. Pescini, G. Rozenberg. - In: THEORETICAL COMPUTER SCIENCE. - ISSN 0304-3975. - 372:2-3(2007 Mar 15), pp. 242-266.
Cycles and communicating classes in membrane systems and molecular dynamics
D. BesozziSecondo
;
2007
Abstract
We are considering sequential membrane systems and molecular dynamics from the viewpoint of Markov chain theory. The configuration space of these systems (including the transitions) is a special kind of directed graph, called a pseudo-lattice digraph, which is closely related to the stoichiometric matrix. Taking advantage of the monoidal structure of this space, we introduce the algebraic notion of precycle. A precycle leads to the identification of cycles by means of the concept of defect, which is a set of geometric constraints on configuration space. Two efficient algorithms for evaluating precycles and defects are given: one is an algorithm due to Contejean and Devie, the other is a novel branch-and-bound tree search procedure. Cycles partition configuration space into equivalence classes, called the communicating classes. The structure of the communicating classes in the free regime–where all rules are enabled–is analyzed: testing for communication can be done efficiently. We show how to apply these ideas to a biological regulatory system.Pubblicazioni consigliate
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