Abstract
We have demonstrated in previous work that the Calculus of Covalent Bonding (CCB) can be used to simulate higher-level biochemical processes. This is significant since CCB was originally devised to model lower-level organic chemical reactions. In this paper we extend the use of the calculus to model an important gene repair pathway, namely DNA Mismatch Repair (MMR). This complex pathway involves four helper proteins and needs a distinction between the two chains in a DNA strand. In order to achieve this, we extend the calculus by allowing prefixing with collections of bonding sites.
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