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A Formalism for the Description of Protein Interaction Dedicated to Jerzy Tiuryn on the Occasion of His Sixty Birthday

Barbuti R., Dezani-Ciancaglini M., Maggiolo-Schettini A., Milazzo P., Troina A.

Fundamenta Informaticae

2010

Vol. 103, nr 1-4

1-29

The Calculus of Looping Sequences is a formalism for describing evolution of biological systems by means of term rewriting rules. We propose to enrich this calculus by labelling elements of sequences. Since two elements with the same label are considered to be linked, this allows us to represent protein interaction at the domain level. Well-formedness of terms are ensured by both a syntactic constraint and a type system: we discuss the differences between these approaches through the description of a biological system, namely the EGF pathway.

A Calculus of Looping Sequences for Modelling Microbiological Systems

Barbuti R., Maggiolo-Schettini A., Milazzo P., Troina A.

Fundamenta Informaticae

2006

Vol. 72, nr 1-3

21-35

The paper presents the Calculus of Looping Sequences (CLS) suitable to describe microbiological systems and their evolution. The terms of the calculus are constructed by basic constituent elements and operators of sequencing, looping, containment and parallel composition. The looping operator allows tying up the ends of a sequence, thus creating a circular sequence which can represent a membrane. We show that a membrane calculus recently proposed can be encoded into CLS. We use our calculus to model interactions among bacteria and bacteriophage viruses, and to reason on their properties.

A Probabilistic Model for Molecular Systems

Barbuti R., Cataudella S., Maggiolo-Schettini A., Milazzo P., Troina A.

Fundamenta Informaticae

2005

Vol. 67, nr 1-3

13--27

We introduce a model for molecular reactions based on probabilistic rewriting rules. We give a probabilistic algorithm for rule applications as a semantics for the model, and we show how a probabilistic transition system can be derived from it. We use the algorithm in the development of an interpreter for the model, which we use to simulate the evolution of molecular systems. In particular, we show the results of the simulation of a real example of enzymatic activity. Moreover, we apply the probabilistic model checker PRISM to the transition system derived by the model of this example, and we show the results of model checking of some illustrative properties.