A framework for protein and membrane interactions

Giorgio Bacci, Davide Grohmann, Marino Miculan

Research output: Contribution to journalConference article in JournalResearchpeer-review

2 Citations (Scopus)
252 Downloads (Pure)

Abstract

We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction levels; in particular, higher-level (e.g. membrane) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. A BioBeta specification provides a protein signature together a set of protein reactions, in the spirit of the kappa-calculus. Moreover, the specification describes when a protein configuration triggers one of the only two membrane interaction allowed, that is "pinch" and "fuse". In this paper we define the syntax and semantics of BioBeta, analyse its properties, give it an interpretation as biobigraphical reactive systems, and discuss its expressivity by comparing with kappa-calculus and modelling significant examples. Notably, BioBeta has been designed after a bigraphical metamodel for the same purposes. Hence, each instance of the calculus corresponds to a bigraphical reactive system, and vice versa (almost). Therefore, we can inherith the rich theory of bigraphs, such as the automatic construction of labelled transition systems and behavioural congruences.
Original languageEnglish
JournalElectronic Proceedings in Theoretical Computer Science
Volume11
ISSN2075-2180
DOIs
Publication statusPublished - 2009
Externally publishedYes
EventWorkshop on Membrane Computing and Biologically Inspired Process Calculi - Bologna, Italy
Duration: 5 Sep 20095 Sep 2009
Conference number: 3

Workshop

WorkshopWorkshop on Membrane Computing and Biologically Inspired Process Calculi
Number3
Country/TerritoryItaly
CityBologna
Period05/09/200905/09/2009

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