On the relationship between membranes and ambients

Ciobanu, Gabriel; Aman, Bogdan

doi:10.1016/j.biosystems.2007.01.006

Cited by 18 publications

(10 citation statements)

References 10 publications

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“…A similar work with this one has been conducted by Ciobanu and Aman in Ciobanu and Aman (2008). They describe a cellular chemical procedure with both membrane systems and safe ambients.…”

Section: Related Workmentioning

confidence: 82%

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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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“…A similar work with this one has been conducted by Ciobanu and Aman in Ciobanu and Aman (2008). They describe a cellular chemical procedure with both membrane systems and safe ambients.…”

Section: Related Workmentioning

confidence: 82%

“…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).…”

Section: Related Workmentioning

confidence: 95%

Membrane automata for modeling biomolecular processes

Giannakis

Andronikos

2015

Nat Comput

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“…In an example of biological modelling using hybrid systems, bisimulation is used to quotient the state space with respect to a subset of variables as a technique for state space reduction [1]. Bisimulation has also been used in the comparison of ambient-style models and membrane-style models [11] and the comparison of a term-rewriting calculus and a simple brane calculus [3]. Other equivalences have been defined for Bio-PEPA.…”

Section: Related and Further Workmentioning

confidence: 99%

A semi-quantitative equivalence for abstracting from fast reactions

Galpin¹,

Hillston²,

Ciocchetta³

2011

Electron. Proc. Theor. Comput. Sci.

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Semantic equivalences are used in process algebra to capture the notion of similar behaviour, and this paper proposes a semi-quantitative equivalence for a stochastic process algebra developed for biological modelling. We consider abstracting away from fast reactions as suggested by the Quasi-Steady-State Assumption. We define a fast-slow bisimilarity based on this idea. We also show congruence under an appropriate condition for the cooperation operator of Bio-PEPA. The condition requires that there is no synchronisation over fast actions, and this distinguishes fast-slow bisimilarity from weak bisimilarity. We also show congruence for an operator which extends the reactions available for a species. We characterise models for which it is only necessary to consider the matching of slow transitions and we illustrate the equivalence on two models of competitive inhibition

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“…In an example of biological modelling using hybrid systems, bisimulation is used to quotient the state space with respect to a subset of variables as a technique for state space reduction [18]. Bisimulation has also been used in the comparison of ambient-style models and membrane-style models [19] and the comparison of a term-rewriting calculus and a simple brane calculus [20].…”

Section: Related Workmentioning

confidence: 99%

Equivalence and Discretisation in Bio-PEPA

Galpin

Hillston

2009

Computational Methods in Systems Biology

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Abstract. Bio-PEPA is a process algebra for modelling biological systems. An important aspect of Bio-PEPA is the ability it provides to discretise concentrations resulting in a smaller, more manageable state space. The discretisation is based on a step size which determines the size of each discrete level and also the maximum number of levels. This paper considers the relationship between two discretisations of the same Bio-PEPA model that differ only in the step size and hence the maximum number of levels, by using the idea of equivalence from concurrency and process algebra. We present a novel behavioural semantic equivalence, compression bisimulation, that equates two discretisations of the same model and we show that this equivalence is a congruence with respect to the synchronisation operator.

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On the relationship between membranes and ambients

Cited by 18 publications

References 10 publications

Membrane automata for modeling biomolecular processes

Membrane automata for modeling biomolecular processes

A semi-quantitative equivalence for abstracting from fast reactions

Equivalence and Discretisation in Bio-PEPA

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