Roberto Barbuti

The calculus of looping sequences

We describe the Calculus of Looping Sequences (CLS) which is suitable for modeling microbiological systems and their evolution. We present two extensions, CLS with links (LCLS) and Stochastic CLS. LCLS simplifies the description of protein interaction at a lower level of abstraction, namely at the domain level. Stochastic CLS allows us to describe quantitative aspects of the modeled systems, such as the frequency of chemical reactions. As examples of application to real biological systems, we show the simulation of the activity of the lactose operon in E.coli and the quorum sensing process in P.aeruginosa, both described with Stochastic CLS.

A general framework for semantics-based bottom-up abstract interpretation of logic programs

The theory of abstract interpretation provides a formal framework to develop advanced dataflow analysis tools. The idea is to define a nonstandard semantics which is able to compute, in finite time, an approximated model of the program. In this paper, we define an abstract interpretation framework based on a fixpoint approach to the semantics. This leads to the definition, by means of a suitable set of operators, of an abstract fixpoint characterization of a model associated with the program. Thus, we obtain a specializable abstract framework for bottom-up abstract interpretations of definite logic programs. The specialization of the framework is shown on two examples, namely, gound-dependence analysis and depth-k analysis.

A transformational approach to negation in logic programming

Abstract A transformation technique is introduced which, given the Horn-clause definition of a set of predicates p i , synthesizes the definitions of new predicate p i which can be used, under a suitable refutation procedure, to compute the finite failure set of p i . This technique exhibits some computational advantages, such as the possibility of computing nonground negative goals still preserving the capability of producing answers. The refutation procedure, named SLDN refutation, is proved sound and complete with respect to the completed program.

Selective Mu-Calculus and Formula-Based Equivalence of Transition Systems

In model checking for temporal logic, the correctness of a system with respect to a desired behavior is verified by checking whether a structure that models the system satisfies a formula describing the behavior. Most existing verification techniques are based on a representation of the system by means of a labeled transition system. In this approach to verification, the efficiency of the model checking is essentially influenced by the number of states of the transition system. In this paper we present a new temporal logic, the selective mu-calculus, and an equivalence between transition systems based on the formulae of this logic. This property preserving equivalence can be used to reduce the size of transition systems. The equivalence (called ?-equivalence) is based on the set, ?, of actions occurring inside the modal operators of a selective mu-calculus formula. We prove that the ?-equivalence coincides with the equivalence induced by the set of the selective mu-calculus formulae with occurring actions in ?. Thus, a formula can be more efficiently checked on a transition system ?-equivalent to the standard one, but smaller than it, since all the actions not in ? are “discarded.”

Spatial P systems

We present Spatial P systems, a variant of P systems which embodies the concept of space and position inside a membrane. Objects in membranes are associated with positions. Rules specify, in the usual way, the objects which are consumed and the ones which are produced; in addition, they can specify the positions of the produced objects. Objects belong to two different sets: the set of ordinary objects and the set of mutually exclusive objects. Every position inside a membrane can accommodate an arbitrary number of ordinary objects, but at most one mutually exclusive object. We prove that Spatial P systems are universal even if only non-cooperating rules are allowed. We also show how Spatial P systems can be used to model the evolution of populations in presence of geographical separations.

Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways

The paper presents the Stochastic Calculus of Looping Sequences (SCLS) suitable to describe microbiological systems, such as cellular pathways, and their evolution. Systems are represented by terms. 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. The evolution of a term is modelled by a set of rewrite rules enriched with stochastic rates representing the speed of the activities described by the rules, and can be simulated automatically. As applications, we give SCLS representations of the regulation process of the lactose operon in Escherichia coli and of the quorum sensing in Pseudomonas aeruginosa . A prototype simulator (SCLSm) has been implemented in F# and used to run the experiments. A public version of the tool is available at the url: http://www.di.unipi.it/~milazzo/biosims/ .

Bisimulations in calculi modelling membranes

Bisimulations are well-established behavioural equivalences that are widely used to study properties of computer science systems. Bisimulations assume the behaviour of systems to be described as labelled transition systems, and properties of a system can be verified by assessing its bisimilarity with a system one knows to enjoy those properties.In this paper we show how semantics based on labelled transition systems and bisimulations can be defined for two formalisms for the description of biological systems, both capable of describing membrane interactions. These two formalisms are the Calculus of Looping Sequences (CLS) and Brane Calculi, and since they stem from two different approaches (rewrite systems and process calculi) bisimulation appears to be a good candidate as a general verification method.We introduce CLS and define a labelled semantics and bisimulations for which we prove some congruence results. We show how bisimulations can be used to verify properties by way of two examples: the description of the regulation of lactose degradation in Escherichia coli and the description of the EGF signalling pathway. We recall the PEP calculus (the simplest of Brane Calculi) and its translation into CLS, we define a labelled semantics and some bisimulation congruences for PEP processes, and we prove that bisimilar PEP processes are translated into bisimilar CLS terms.

Bisimulation congruences in the calculus of looping sequences

The Calculus of Looping Sequences (CLS) is a calculus suitable to describe biological systems and their evolution. CLS terms are constructed by starting from basic constituents and composing them by means of operators of concatenation, looping, containment and parallel composition. CLS terms can be transformed by applying rewrite rules. We give a labeled transition semantics for CLS by using, as labels, contexts in which rules can be applied. We define bisimulation relations that are congruences with respect to the operators on terms, and we show an application of CLS to the modeling of a biological system and we use bisimulations to reason about properties of the described system.

Compositional semantics and behavioral equivalences for P Systems

The aim of the paper is to give a compositional semantics in the style of the Structural Operational Semantics (SOS) and to study behavioral equivalence notions for P Systems. Firstly, we consider P Systems with maximal parallelism and without priorities. We define a process algebra, called P Algebra, whose terms model membranes, we equip the algebra with a Labeled Transition System (LTS) obtained through SOS transition rules, and we study how some equivalence notions defined over the LTS model apply in our case. Then, we consider P Systems with priorities and extend the introduced framework to deal with them. We prove that our compositional semantics reflects correctly maximal parallelism and priorities.

Checking security of Java bytecode by abstract interpretation

We present a method to certify a subset of the Java bytecode, with respect to security. The method is based on abstract interpretation of the operational semantics of the language. We define a concrete small-step enhanced semantics of the language, able to keep information on the flow of data and control during execution. A main point of this semantics is the handling of the influence of the information flow on the operand stack. We then define an abstract semantics, keeping only the security information and forgetting the actual values. This semantics can be used as a static analysis tool to check security of programs. The use of abstract interpretation allows, on one side, being semantics based, to accept as secure a wide class of programs, and, on the other side, being rule based, to be fully automated.