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Genetic Systems are a formalism inspired by genetic regulatory networks, suitable for modeling the interactions between genes and proteins, acting as regulatory products. The evolution is driven by genetic gates: a new object (representing a protein) is produced when all activator objects are available in the system, and no inhibitor object is present. Activators are not consumed by the application of such a rule. Objects disappear because of degradation: each object is equipped with a lifetime, and the object decays when such a lifetime expires. It is known that such systems are Turing powerful, either when we consider interleaving semantics (a single action is executed in each computational step) as well as if we consider maximal parallel semantics (all the rules that can be applied at a computational step must be applied). In this paper we investigate the power of inhibiting rules. © 2009 Springer-Verlag Berlin Heidelberg.

We introduce Genetic Systems, a formalism inspired by genetic regulatory networks and suitable for modeling the interactions between the genes and the proteins, acting as regulatory products. The generation of new objects, representing proteins, is driven by genetic gates: a new object is produced when all the activator objects are available in the system, and no inhibitor object is available. Activators are not consumed by the application of such an evolution rule. Objects disappear because of degradation: each object is equipped with a lifetime, and the object decays when such a lifetime expires. We investigate the computational expressiveness of Genetic Systems: we show that they are Turing equivalent by providing encodings of Random Access Machines in Genetic Systems. © 2008 Elsevier B.V. All rights reserved.

In recent years, the modeling and analysis techniques developed in the area of formal languages and of concurrent process calculi have been successfully applied to the field of Systems Biology. In this setting, Brane Calculi and Membrane Systems are two of the most prominent approaches for the modeling of the behaviour of biological membranes. Membrane Systems have been introduced by Gh. Pǎun as a class of distributed parallel computing devices of a biochemical type, while Brane Calculi are a family of process calculi, based on a set of biologically inspired primitives of membrane interaction. In this paper we model the behaviour of a biological process - namely, the LDL Cholesterol Degradation Pathway - in both Brane Calculi and Membrane Systems. We also provide a brief discussion on the application of analysis techniques to this case study. © 2006 IEEE.

We consider the structure of the intestinal epithelial tissue and of cellcell junctions as the biological model inspiring a new class of P systems. First we define the concept of cell polarity, a formal property derived from epithelial cells, which present morphologically and functionally distinct regions of the plasma membrane. Then we show two preliminary results for this new model of computation: on the theoretical side, we show that P systems with cell polarity are computationally (Turing) complete; on the modelling side, we show that the transepithelial movement of glucose from the intestinal lumen into the blood can be described by such a formal system. Finally, we define tissue P systems with cell polarity, where each cell has fixed connections to the neighbouring cells and to the environment, according to both the cell polarity and specific cellcell junctions. © 2009 Cambridge University Press.

Genetic Systems are a formalism inspired by genetic regulatory networks, suitable for modeling the interactions between genes and proteins, acting as regulatory products. The evolution is driven by genetic gates: a new object (representing a protein) is produced when all activator objects are available in the system, and no inhibitor object is present. Activators are not consumed by the application of such a rule. Objects disappear because of degradation: each object is equipped with a lifetime, and the object decays when such a lifetime expires. We investigate the computational expressiveness of Genetic Systems with interleaving semantics (a single action is executed in a computational step): we show that they are Turing equivalent by providing a deterministic encoding of Random Access Machines in Genetic Systems. We also show that the computational power strictly decreases when moving to Genetic Systems where either the degradation or the inhibition mechanism are absent

We introduce Genetic P systems, a class of P systems with evolution rules inspired by the functioning of the genes. The creation of new objects - representing proteins - is driven by genetic gates: a new object is produced when all the activator objects are present, and no inhibitor object is available. Activator objects are not consumed by the application of such an evolution rule. Objects disappear because of degradation: each object is equipped with a lifetime; when such a lifetime expires, the object decays. Then, we extend the basic model with bind and release rules and repressor rules, that simulate the action of protein channels and the action of substances which connect to other objects to block their use. We provide a universality result for such a class of systems. © Springer-Verlag Berlin Heidelberg 2006

We propose a functorial concurrent semantics for Petri nets extended with read and inhibitor arcs, that we call inhibitor nets. Along the lines of the seminal work of Winskel on safe nets and extending a previous work in [1] for nets with read arcs, the truly concurrent semantics is given at a categorical level via a chain of functors leading from the category SW-IN of semi-weighted inhibitor nets to the category Dom of finitary prime algebraic domains (equivalent to the category PES of prime event structures). As an intermediate semantic model, we introduce inhibitor event structures, an extension of prime event structures able to faithfully capture the dependencies among events which arise in the presence of read and inhibitor arcs. [1] P. Baldan, A. Corradini, U. Montanari "An Event Structure Semantics for P/T Contextual Nets: Asymmetric Event Structures" FoSSaCS '98 Conference Proceedings, Springer LNCS vol. 1378, 1998, pp. 63-80.