5 research outputs found
A Global Occurrence Counting Analysis for Brane Calculi
We propose a polynomial static analysis for Brane Calculi, based on Abstract Interpretation techniques. The analysis provides a description of the possible hierarchical structure of membranes and of the processes possibly associated to each membrane, together with global occurrence counting information. Our analysis
can be applied in the biological setting to investigate systems in which the information
on the number of membranes occurring in the system plays a crucial role
Generalized contexts for reaction systems: definition and study of dynamic causalities
Reaction systems are a qualitative formalism for the modelling of systems of biochemical reactions. In their original formulation, a reaction system executes in an environment (or context) that can supply it with new objects at each evolution step. The context drives the behaviour of a reaction system: it can provide different inputs to the system that can lead to different behaviours. In order to more faithfully deal with open systems, in this paper we propose a more powerful notion of context having not only the capability to provide objects, but also to absorb (or remove) objects at each evolution step. For such reaction systems with generalized context we investigate properties of dynamic causality by revising the previously proposed concept of formula based predictor. A formula based predictor is a Boolean formula characterising all contexts that lead to the production of a certain object after a given number of steps. In this paper, we revise the theory of formula based predictors in order to deal with reaction systems executed in a context of the new kind. As applications, we show an example of interaction between biochemical pathways and a reaction system modelling cell metabolism and respiration
A Formal Approach to Open Multiparty Interactions
We present a process algebra aimed at describing interactions that are
multiparty, i.e. that may involve more than two processes and that are open,
i.e. the number of the processes they involve is not fixed or known a priori.
Here we focus on the theory of a core version of a process calculus, without
message passing, called Core Network Algebra (CNA). In CNA communication
actions are given not in terms of channels but in terms of chains of links that
record the source and the target ends of each hop of interactions. The
operational semantics of our calculus mildly extends the one of CCS. The
abstract semantics is given in the style of bisimulation but requires some
ingenuity. Remarkably, the abstract semantics is a congruence for all operators
of CNA and also with respect to substitutions, which is not the case for strong
bisimilarity in CCS. As a motivating and running example, we illustrate the
model of a simple software defined network infrastructure.Comment: 62 page
A static analysis for Brane Calculi providing global occurrence counting information
In this paper we propose a static analysis for Brane Calculi [1], based on Abstract Interpretation [2] techniques. Our analysis statically approximates the dynamic behaviour of Brane systems, by providing a description of the possible hierarchical structure of membranes and of the processes possibly associated to each membrane, together with global occurrence counting information. Our analysis can be computed in polynomial time. We apply it to investigate several biological systems in which occurrence counting information plays a crucial role. In particular, our case study concerns the formation of the haemoglobin polymer in presence of alterations and investigate the influence that such alterations have on the ability of the haemoglobin polymer to bind oxygen molecules
An Analysis for Causal Properties of Membrane Interactions
AbstractWe present here an analysis, based on Abstract Interpretation [P. Cousot and R. Cousot. Abstract Interpretation: A Unified Lattice Model for Static Analysis of Programs by Construction or Approximation of Fixpoints. In Proc. Fourth ACM Symp. Principles of Programming Languages (POPLʼ77), pp. 238–252, 1977.], obtained by defining a finite computable approximation of the causal semantics proposed in [N. Busi. Towards a Causal Semantics for Brane Calculi. In What is it About Government that Americans Dislike, pp. 1945–1965, University Press, 2007.] for the Mate/Bud/Drip (MBD) Brane Calculus [L. Cardelli. Brane calculi - interactions of biological membranes. In Proc. of Computational Methods in Systems Biology (CMSBʼ04), LNCS 3082, pp. 257–280, 2005.]. The causal semantics in [N. Busi. Towards a Causal Semantics for Brane Calculi. In What is it About Government that Americans Dislike, pp. 1945–1965, University Press, 2007.] is able to address different kinds of causal dependencies: structural, synchronisation and the so-called environment causality. Our analysis, being a safe (over)-approximation of such causal semantics, besides modelling all possible evolutions of the system, can be used to formally prove causal properties among membrane interactions