A bioambients based framework for chain-structured biomolecules modelling

Authors:
Cheng Fu;Zhengwei Qi;Jinyuan You
Affiliations:
Dept. of Computer Science and Engineering, Shanghai Jiao Tong Univ., China;Dept. of Computer Science and Engineering, Shanghai Jiao Tong Univ., China;Dept. of Computer Science and Engineering, Shanghai Jiao Tong Univ., China
Venue:
CIS'04 Proceedings of the First international conference on Computational and Information Science
Year:
2004

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Abstract

This paper presents a formal extension to describe simple chain-like biomolecular structures and related operations based on the calculus of BioAmbients which serves as a basic framework to model compartments. In our extension, we represent these biomolecules by means of an abstract chain structure possibly with paired molecules at each node, including the effect between molecules, the intra interaction and movement inside linked molecules, and the inter interaction and movement between linked molecules and general compartments. Moreover, An example is given to model the one of the major phases during the process of protein synthesis.