A framework for protein and membrane interactions

dels 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 Bio specification provides a protein signature together a set of protein reactions, in the spirit of the -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 Bio, analyse its properties, give it an interpretation as biobigraphical reactive systems, and discuss its expressivity by comparing with calculus and modelling significant examples. Notably, Bio 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 constructio...

• Type: Journal
• Year: 2009
• Where: CORR
• Authors: Giorgio Bacci, Davide Grohmann, Marino Miculan
• Keywords: Biobigraphical Reactive Systems, CORR 2009, Education, Formal Biological Justification, Protein