Decision problems in 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 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 be moved between the regions of the system. Moreover, in each region there are evolution rules that rewrite the transported objects, mimicking chemical reactions. We investigate qualitative properties, like configuration reachability, in relation to the use of cooperative or non-cooperative evolution and transport rules and in the contexts of free- and maximal-parallel evolution. © 2008.