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Turing Universality of the Biochemical Ground Form
 UNDER CONSIDERATION FOR PUBLICATION IN MATH. STRUCT. IN COMP. SCIENCE
, 2009
"... We explore the expressive power of languages that naturally model biochemical interactions with relative to languages that naturally model only basic chemical reactions, identifying molecular association as the basic mechanism that distinguishes the former from the latter. We use a process algebra, ..."
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Cited by 7 (2 self)
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We explore the expressive power of languages that naturally model biochemical interactions with relative to languages that naturally model only basic chemical reactions, identifying molecular association as the basic mechanism that distinguishes the former from the latter. We use a process algebra, the Biochemical Ground Form (BGF), which extends with primitives for molecular association CGF, a process algebra proved to be equivalent to the traditional notations for describing basic chemical reactions. We first observe that, differently from CGF, BGF is Turing universal as it supports a finite precise encoding of Random Access Machines, a wellknown Turing powerful formalism. Then we prove that the Turing universality of BGF derives from the interplay between the molecular primitives of association and dissociation. In fact, the elimination from BGF of the primitives already present in CGF does not reduce the computational strength of the process algebra, while if either association or dissociation is removed then BGF is no longer Turing complete.
On the Decidability Status of Reachability and Coverability in Graph Transformation Systems
, 2012
"... We study decidability issues for reachability problems in graph transformation systems, a powerful infinitestate model. For a fixed initial configuration, we consider reachability of an entirely specified configuration and of a configuration that satisfies a given pattern (coverability). The former ..."
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Cited by 4 (1 self)
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We study decidability issues for reachability problems in graph transformation systems, a powerful infinitestate model. For a fixed initial configuration, we consider reachability of an entirely specified configuration and of a configuration that satisfies a given pattern (coverability). The former is a fundamental problem for any computational model, the latter is strictly related to verification of safety properties in which the pattern specifies an infinite set of bad configurations. In this paper we reformulate results obtained, e.g., for contextfree graph grammars and concurrency models, such as Petri nets, in the more general setting of graph transformation systems and study new results for classes of models obtained by adding constraints on the form of reduction rules.
Parameterized Verification of Graph Transformation Systems with Whole Neighbourhood Operations
, 2014
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Hunting distributed malware with the κcalculus
"... Abstract. The defense of computer systems from malicious software attacks, such as viruses and worms, is a key aspect of computer security. The analogy between malicious software and biological infections suggested us to use the κcalculus, a formalism originally developed for the analysis of biolog ..."
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Abstract. The defense of computer systems from malicious software attacks, such as viruses and worms, is a key aspect of computer security. The analogy between malicious software and biological infections suggested us to use the κcalculus, a formalism originally developed for the analysis of biological systems, for the formalization and analysis of malicious software. By modeling the different actors involved in a malicious code attack in the κcalculus and by simulating their behavior, it is possible to extract important information that can drive in the choice of the defense technique to apply. 1
Under consideration for publication in Math. Struct. in Comp. Science Equilibrium and Termination II: the case of
, 2011
"... This paper is concerned with the asymptotic properties of a restricted class of Petri nets equipped with stochastic mass action semantics. We establish a simple algebraic criterion for the existence of an equilibrium, that is to say an invariant probability that satisfies the detailed balance condit ..."
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This paper is concerned with the asymptotic properties of a restricted class of Petri nets equipped with stochastic mass action semantics. We establish a simple algebraic criterion for the existence of an equilibrium, that is to say an invariant probability that satisfies the detailed balance condition familiar from the thermodynamics of reaction networks. We also find that when such a probability exists, it can be described by a free energy function which combines an internal energy term and an entropy one. Under strong additional conditions, we show how the entropy term can be deconstructed using the finergrained individualtoken semantics of Petri nets. 1.
Towards a minimal calculus for complexation
"... Abstract. We present here a termination preserving encoding of Minsky Machines in a particularly restricted fragment of the κcalculus where only one species with no fields is admitted and only binary rules are allowed. 1 ..."
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Abstract. We present here a termination preserving encoding of Minsky Machines in a particularly restricted fragment of the κcalculus where only one species with no fields is admitted and only binary rules are allowed. 1
Complex Functional Rates in the Modeling of Nano Devices (Extended abstract)
, 2013
"... We give an overview of recent work on the rulebased modeling of nano devices. In particular, our experience in the modeling of a nanoscale elevator suggested us to enhance rulebased modeling with complex functional rates that can be used to express rates that depend on the current state of the ent ..."
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We give an overview of recent work on the rulebased modeling of nano devices. In particular, our experience in the modeling of a nanoscale elevator suggested us to enhance rulebased modeling with complex functional rates that can be used to express rates that depend on the current state of the entire complexes in which the reacting molecules reside.
Research activity during and father the PhD Dossier n. 48773
, 2011
"... Bologna (Italy). I have been selected for this position and the course started in January 2005, under the supervision of Prof. Maurizio Gabbrielli. The first three years have been funded by a government scholarship. The last year, instead, I have applied for a scholarship (Assegno di ricerca) funded ..."
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Bologna (Italy). I have been selected for this position and the course started in January 2005, under the supervision of Prof. Maurizio Gabbrielli. The first three years have been funded by a government scholarship. The last year, instead, I have applied for a scholarship (Assegno di ricerca) funded by the University of Bologna. Since the beginning of my career as a PhD student I have been interested in the general topic of concurrency theory. More precisely I have been interested in studying how the different constructs of concurrent languages influence their expressiveness and which are the techniques to identify the gaps of expressiveness. The influence of nondeterminism. At the beginning, inspired by the works by Plotkin [9, 10], we decided to focus on how a particular form of non determinism affects the expressiveness of a variant of Milner’s CCS. In this variant, replication is used instead of recursion. The relative expressiveness of the two calculi was studied in [3]. We were interested in further investigate