Fig 1. Examples of compartmental dynamics in cell biology.

The figure shows a sketch of the processes, the specification in ML-Rules 3, and the n-ary tree structure of the term rewriting that underlies ML-Rules interpretation. The red lines in the n-ary tree structure indicate structures that are changed during the reaction. For the rules, we use the ML-Rules notation. The left side is transformed (using the →) into the right side at a rate (following the @ symbol). The {} denote nesting relationships. (a) Fission and fusion of compartments: A large mitochondrium can divide into two smaller ones, whereby its content (here ?M1 and ?M2) is distributed between the two new mitochondria. Two mitochondria can also fuse into a large one containing the solution of both smaller ones. (b) Creation and removal of compartments: During the endocytosis of the lipoplex, an endosome is formed around it. Inside the cell, the lipoplex can unpack its content (?L) into the cell. (c) Shuttling of compartments: A virus carrying DNA or RNA can enter a cell. New viruses produced in the cell can level it and spread.