Molecular Structures

Gabriel Ciobanu ()
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Gabriel Ciobanu: A.I. Cuza University, Faculty of Computer Science

Chapter Chapter 27 in Where Mathematics, Computer Science, Linguistics and Biology Meet, 2001, pp 299-317 from Springer

Abstract: Abstract We introduce an abstract molecular structure, then we describe the DNA methylation by using a known calculus of the communicating concurrent systems, namely the π-calculus. Finally, we show that it is possible to have a well-defined interpretation of the π-terms by using our abstract molecular structures. In this way we introduce and study some abstract structures which are similar to the abstract machines in computer science (as Turing machines or automata), and suitable to express molecular interactions. We should remark that the considered interactions imply modifications too (e.g. DNA methylation); in order to express this aspect, we consider and study interactions with substitutions. Because the covalent bounds play a special role when we refer to DNA, our abstract molecular structures are systems with joined (shared) resources; they emphasize the use of some shared resources, as well as the resource transitions. Formally, we use some notions and results of concurrency theory, particularly π-calculus and multiset semantics.

Keywords: Turing Machine; Abstract Machine; Reaction Rule; Covalent Bound; Resource Transition (search for similar items in EconPapers)
Date: 2001
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Persistent link: https://EconPapers.repec.org/RePEc:spr:sprchp:978-94-015-9634-3_27

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DOI: 10.1007/978-94-015-9634-3_27

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