Using Rewriting Techniques in the Simulation of Dynamical Systems: Application to the Modeling of Sperm Crawling
Rewriting system (RS) are a formalism widely used in computer science. However, such a formalism can also be used to specify executable models of dynamical systems (DS) by allowing the specification of the evolution laws of the systems in a local manner.
The main drawback of RS is that they are well understood and well known only for terms (a tree-like structure) and that their expressivity is not enough for the representation of complex organizations that can be found in DS.
We propose a framework based on topological notion to extend the notion of RS on more sophisticated structures; the corresponding concepts are validated through the development of an experimental programming language, MGS, dedicated to the simulation of DS. We show how the MGS rewriting system can be used to specify complex dynamical systems and illustrate it with the simulation of the motility of the nematode’s sperm cell.
Unable to display preview. Download preview PDF.
- 2.Bottino, D., Mogilner, A., Roberts, T., Stewart, M., Oster, G.: How nematode sperm crawl. Journal of Cell Science 115, 367–384 (2002)Google Scholar
- 3.Dershowitz, N., Jouannaud, J.P.: Rewrite systems. Handbook of Theoretical Computer Science, vol. B, pp. 244–320. Elsevier Science, Amsterdam (1990)Google Scholar
- 4.Giavitto, J.L., Godin, C., Michel, O., Prusinkiewicz, P.: Computational Models for Integrative and Developmental Biology. In: Modelling and Simulation of biological processes in the context of genomics, Hermes (2002)Google Scholar
- 6.Bottino, D.: Ascaris suum sperm model documentation (2000)Google Scholar