A Uniform Framework of Molecular Interaction for an Artificial Chemistry with Compartments

Cells have acquired a complex membrane structure through evolution. Each compartment separated by membranes has its specific functions, and the coordination of those functions constitutes the behaviour of the living system at a biochemical level. Therefore, it is necessary for an artificial chemistry to have an ability to express membrane structures if it is to be used to study such behaviour. In this paper, we propose a way of incorporating nested membrane structures in an artificial chemistry. This extension is achieved mainly by adding the following two components to the formalism: one is membranes, which is not only a boundary between two reaction pools but is also a reaction pool itself; the other is membrane molecules, which are embedded in a membrane and change their forms by recombination rules. The introduction of membrane molecules enables the formalism to deal with the movement of molecules across a membrane in a similar way as reaction between normal molecules. Using the extended artificial chemistry, we modelled two functions in natural living systems, namely, signal transduction and intracellular transport, and thereby show the advantages of the present approach to introducing compartments to artificial chemistries