Modelling Cellular Processes using Membrane Systems with Peripheral and Integral Proteins

Membrane systems were introduced as models of computation inspired by the structure and functioning of biological cells. Recently, membrane systems have also been shown to be suitable to model cellular processes. We introduce a new model called Membrane Systems with Peripheral and Integral Proteins. The model has compartments enclosed by membranes, floating objects, objects associated to the internal and external surfaces of the membranes and also objects integral to the membranes. The floating objects can be processed within the compartments and can interact with the objects associated to the membranes. The model can be used to represent cellular processes that involve compartments, surface and integral membrane proteins, transport and processing of chemical substances. As examples we model a circadian clock and the G-protein cycle in yeast saccharomyces cerevisiae and present a quantitative analysis using an implemented simulator. This is a preliminary version of a paper that was published in Proceedings of the International Conference on Computational Methods in Systems Biology, CMSB06, Lecture Notes in Bioinformatics, 4210:108-126, 2006. The original publication is available at www.springerlink.com