Membrane Systems with Peripheral Proteins: Transport and Evolution

Transport of substances and communication between compartments are fundamental biological processes, often mediated by the presence of opportune and complementary proteins attached to the surfaces of membranes. Within compartments, substances are acted upon by local biochemical rules. Inspired by this behaviour we present a model based on membrane systems, with objects attached to the sides of the membranes and floating objects that can move between the regions of the system. Moreover, in each region there are evolution rules that rewrite the transported objects, mimicking chemical reactions. We first analyse the system, showing that interesting qualitative properties can be decided (like reachability of configurations) and then present a simulator based on a stochastic version of the introduced model and show how it can be used to simulate relevant quantitative biological processes. This is a preliminary version of a paper that was published in Proceedings of MeCBIC06, Electronic Notes in Theoretical Computer Science, 171:2, 37-53, 2007. The original version can be found at http://www.elsevier.com/wps/find/journaldescription.cws_home/681021/description#description