Bigraphical models for protein and membrane interactions

Giorgio Bacci, Davide Grohmann, Marino Miculan

Research output: Contribution to journalConference article in JournalResearchpeer-review

7 Citations (Scopus)
224 Downloads (Pure)

Abstract

We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules representing biologically admissible interactions. At the protein level, these bigraphic reactive systems correspond exactly to systems of kappa-calculus. Membrane-level interactions are represented by just two general rules, whose application can be triggered by protein-level interactions in a well-defined and precise way. This framework can be used to compare and merge models at different abstraction levels; in particular, higher-level (e.g. mobility) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. As examples, we formalize in our framework the vesiculation and the phagocytosis processes.
Original languageEnglish
JournalElectronic Proceedings in Theoretical Computer Science
Volume11
Pages (from-to)3-18
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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