title: Converting differential-equation models of biological systems to membrane computing.
abstract: This paper presents a method to convert the deterministic, continuous representation of a biological system by ordinary differential equations into a non-deterministic, discrete membrane computation. The dynamics of the membrane computation is governed by rewrite rules operating at certain rates. That has the advantage of applying accurately to small systems, and to expressing rates of change that are determined locally, by region, but not necessary globally. Such spatial information augments the standard differentiable approach to provide a more realistic model. A biological case study of the ligand-receptor network of protein TGF-β is used to validate the effectiveness of the conversion method. It demonstrates the sense in which the behaviours and properties of the system are better preserved in the membrane computing model, suggesting that the proposed conversion method may prove useful for biological systems in particular.
authors.affiliation: Research Center for Software Technology and Management, Faculty of Technology and Information Science, National University of Malaysia, 43600 Bangi, Selangor, Malaysia. Electronic address: ravie@ftsm.ukm.my.
authors.forename: Ravie Chandren
authors.initials: RC
authors.lastname: Muniyandi
authors.forename: Abdullah Mohd
authors.initials: AM
authors.lastname: Zin
authors.forename: J W
authors.initials: JW
authors.lastname: Sanders
mesh_terms: D019295:Computational Biology / Q000379:methods*; D039301:Computers, Molecular / Q000639:trends*; D008024:Ligands; D008954:Models, Biological; D049490:Systems Biology / Q000379:methods*; D016212:Transforming Growth Factor beta / Q000378:metabolism*
chemical_list: D008024:Ligands; D016212:Transforming Growth Factor beta
keywords: Ligand–receptor network of TGF-β; Membrane computing; Modelling biological systems; Ordinary differential equations; Rewrite rules