An Analysis for Causal Properties of Membrane 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.

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“…[φ] \ , since φ distributes over the single links. Therefore, weobtain that s 0 [φ] s 0 [φ] \ .We recall Lemma 20 (the original appears on p 19)…”

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confidence: 99%

A formal approach to open multiparty interactions

Bodei

Brodo

Bruni

2019

Theoretical Computer Science

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“…Both scenarios correspond to real biological behaviours, as detailed at the end of Section 3. While polynomial analyses such as the ones in [6,7,3,8,9] would predict the same hierarchical structure for both scenarios, our analysis is able to predict that the first scenario corresponds to a one-to-one interaction between a vesicle and the target membrane, while the second scenario models a one-to-many interaction among a vesicle and the target membrane. Therefore, thanks to the occurrence counting information, our analysis succeeds in capturing the relevant difference in the behaviour of the two systems.…”

Section: Introductionmentioning

confidence: 75%

“…the survey in [10]). In particular, Control Flow Analysis (CFA) has been applied to Betabinders [11] in [7], to Brane Calculi [3], and to BioAmbients [12] in [6,8,13,14]; while Abstract Interpretation to BioAmbients [15,16,17], to Brane Calculi [9,18] and to Reaction Systems [19,20]. Many of these works are inspired by the application of static analysis techniques [21,22,23] to Mobile Ambients (MA) [24], from which, many bio-inspired calculi derive.…”

Section: Introductionmentioning

confidence: 99%

“…These techniques have polynomial complexity but they provide a less precise description of the possible topological structure of derivatives given that they do not maintain any information on occurrence counting. The richer contextual CFA in [13], and the AI-based analyses in [9,18] improve the prediction accuracy, but, still, they are not able to observe the multiplicity. In particular, the analyses in [9,18] provide an abstract version of the causal semantics for Brane Calculi proposed by Busi [25].…”

Section: Introductionmentioning

confidence: 99%

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A static analysis for Brane Calculi providing global occurrence counting information

Bodei

Brodo

Gori

et al. 2017

Theoretical Computer Science

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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.

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“…Besides the work in Ciobanu and Aman (2008), a similar work with this one was in Cardelli and Pȃun (2006) where they combined membrane computing concepts with brane calculus (Cardelli 2005). Brane calculus was related with the mitochondrial fusion mechanism in Bodei et al (2013). In Alexiou et al (2011) the authors proposed a model describing the fusion of two mitochondria.…”

Section: Related Workmentioning

confidence: 98%

Membrane automata for modeling biomolecular processes

Giannakis

Andronikos

2015

Nat Comput

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Bioinspired computation models and mechanisms are widely used in various applications, both in theoretical and practical level. Membrane Computing, a branch of Natural Computing, is constantly producing interesting results the last 15 years. In this work we attempt to describe a mitochondrial fusion process based on membrane automata in a novel way. We combine these computation machines with notions from brane calculus and we depict the procedure of the production of specific proteins that are essential for a successful fusion. We also discuss possible extensions of our methodology stating direction for future works and thoughts.

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An Analysis for Causal Properties of Membrane Interactions

Cited by 11 publications

References 6 publications

A formal approach to open multiparty interactions

A formal approach to open multiparty interactions

A static analysis for Brane Calculi providing global occurrence counting information

Membrane automata for modeling biomolecular processes

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