Simulation of Base Excision Repair in the Calculus of Covalent Bonding

摘要

In previous papers we have introduced a new process calculus inspired by chemical reactions, called the Calculus of Covalent Bonding. The key feature of the calculus was a new prefix operator of the form (s;b), where doing of action b triggers undoing of one of the actions in s. Because of this connection between doing and undoing of actions (or forming and breaking of bonds in a chemical modelling) we called this local reversibility. We have shown that our calculus enables out-of-causal order reversibility. In this paper we demonstrate the Base Excision Repair of DNA, a high-level biological example, using our calculus. We also introduce a software which allows us to check the syntax of processes and to simulate their execution.