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1
Content available remote Specialized Predictor for Reaction Systems with Context Properties
Barbuti R., Gori R., Levi F., Milazzo P.
Fundamenta Informaticae
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2016
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Vol. 147, nr 2/3
173--191
EN
Reaction systems are a qualitative formalism for modeling systems of biochemical reactions characterized by the non-permanency of the elements: molecules disappear if not produced by any enabled reaction. Reaction systems execute in an environment that provides new molecules at each step. Brijder, Ehrenfeucht and Rozemberg introduced the idea of predictors. A predictor of a molecule s, for a given n, is the set of molecules to be observed in the environment to determine whether s is produced or not at step n by the system. We introduced the notion of formula based predictor, that is a propositional logic formula that precisely characterizes environments that lead to the production of s after n steps. In this paper we revise the notion of formula based predictor by defining a specialized version that assumes the environment to provide molecules according to what expressed by a temporal logic formula. As an application, we use specialized formula based predictors to give theoretical grounds to previously obtained results on a model of gene regulation.
2
Content available remote On Conditions for Modular Verification in Systems of Synchronising Components
Drábik P., Maggiolo-Schettini A., Milazzo P.
Fundamenta Informaticae
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2012
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Vol. 120, nr 3/4
259-274
EN
Property preservation is investigated as an approach to modular verification, leading to reduction of the property verification time for formal models. For modelling purposes, formalisms with multi-way synchronisations are considered. For the modular verification technique to work, a specific type of synchronisation is required for which a sufficient and necessary condition is identified. It is a requirement on the semantics of the formalism, which is restricted to permit simultaneous execution only of component moves that make reference to each other. Implications for modular verification of several well-known formalisms for concurrent systems are investigated.
3
Content available remote Maximally Parallel Probabilistic Semantics for Multiset Rewriting
Barbuti R., Levi F., Milazzo P., Scatena G.
Fundamenta Informaticae
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2011
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Vol. 112, nr 1
1-17
EN
Maximally parallel semantics have been proposed for many formalisms as an alternative to the standard interleaving semantics for some modelling scenarios. Nevertheless, in the probabilistic setting an affirmed interpretation of maximal parallelism still lacks. We define a synchronous maximally parallel probabilistic semantics for multiset rewriting tailored to describe, simulate and verify biological systems evolving with maximally parallel steps. Each step of the proposed semantics is parallel as each reaction can happen multiple times, and it is maximal as it leaves no enabled reaction i.e. as many reactions as possible are executed. We define a maximally parallel probabilistic semantics in terms of Discrete Time Markov Chain for systems described by stochastic multiset rewriting. We propose a simple, maximally parallel, model of Caenorhabditis elegans vulval development on which we show probabilistic simulations results.
4
Content available remote A Notion of Biological Diagnosability Inspired by the Notion of Opacity in Systems Security
Barbuti R., Maggiolo-Schettini A., Milazzo P., Gruska D.P.
Fundamenta Informaticae
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2010
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Vol. 102, nr 1
19-34
EN
A formal model for diagnostics of biological systems modelled as P systems is presented. We assume the presence of some biologically motivated changes (frequently pathological) in the systems behavior and investigate when these changes could be diagnosed by an external observer by exploiting some techniques originally developed for reasoning on system security.
5
Content available remote 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
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2010
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Vol. 103, nr 1-4
1-29
EN
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.
6
Content available remote Timed P Automata
Barbuti R., Maggiolo-Schettini A., Milazzo P., Tesei L.
Fundamenta Informaticae
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2009
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Vol. 94, nr 1
1-19
EN
To study systems whose dynamics changes with time, an extension of timed P systems is introduced in which evolution rules may vary with time. The proposed model is a timed automaton with a discrete time domain and in which each state is a timed P system. A result on expressive power and on features of the formalism sufficient for full expressiveness is proved and, as an application example, the model of an ecological system is given.
7
Content available remote P Systems with Transport and Diffusion Membrane Channels
Barbuti R., Maggiolo-Schettini A., Milazzo P., Tini S.
Fundamenta Informaticae
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2009
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Vol. 93, nr 1-3
17-31
EN
P Systems are computing devices inspired by the structure and the functioning of a living cell. A P System consists of a hierarchy of membranes, each of them containing a multiset of objects, a set of evolution rules, and possibly other membranes. Evolution rules are applied to the objects of the same membrane with maximal parallelism. In this paper we present an extension of P Systems, called P Systems with Membrane Channels (PMC Systems), in which membranes are enriched with channels and objects can pass through a membrane only if there are channels on the membrane that enable such a passage. We show that PMC Systems are universal even if only the simplest form of evolution rules is considered, and we give two application examples.
8
Content available remote Security in a Model for Long-running Transactions
Gruska D.P., Maggiolo-Schettini A., Milazzo P.
Fundamenta Informaticae
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2008
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Vol. 85, nr 1-4
189-203
EN
Communicating Hierarchical Transaction-based Timed Automata have been introduced to model systems performing long-running transactions. Here, for these automata a security concept is introduced, which is based on a notion of opacity and on the assumption that an attacker can not only observe public system activities, but also cause abortion of some of them. Different intruder capabilities as well as different kinds of opacity are defined and the resulting security properties are investigated. Security of long-running transactions is defined by the mentioned notion of opacity and conditions for compositionality are established.
9
Content available remote A P Systems Flat Form Preserving Step-by-step Behaviour
Barbuti R., Maggiolo-Schettini A., Milazzo P., Tini S.
Fundamenta Informaticae
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2008
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Vol. 87, nr 1
1-34
EN
Starting from a compositional operational semantics of transition P Systems we have previously defined, we face the problem of developing an axiomatization that is sound and complete with respect to some behavioural equivalence. To achieve this goal, we propose to transform the systems into a normal form with an equivalent semantics. As a first step, we introduce axioms which allow the transformation of membrane structures into flat membranes. We leave as future work the further step that leads to the wanted normal form.
10
Content available remote A Calculus of Looping Sequences for Modelling Microbiological Systems
Barbuti R., Maggiolo-Schettini A., Milazzo P., Troina A.
Fundamenta Informaticae
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2006
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Vol. 72, nr 1-3
21-35
EN
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.
11
Content available remote A Probabilistic Model for Molecular Systems
Barbuti R., Cataudella S., Maggiolo-Schettini A., Milazzo P., Troina A.
Fundamenta Informaticae
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2005
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Vol. 67, nr 1-3
13--27
EN
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.
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