Abstract
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.
The author acknowledges partial support of COST Action IC1405 on Reversible Computation - extending horizons of computing.
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References
Aman, B., Ciobanu, G.: Controlled reversibility in reaction systems. In: Gheorghe, M., Rozenberg, G., Salomaa, A., Zandron, C. (eds.) CMC 2017. LNCS, vol. 10725, pp. 40–53. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-73359-3_3
Köhler, A., Krivine, J., Vidmar, J.: A rule-based model of base excision repair. In: Mendes, P., Dada, J.O., Smallbone, K. (eds.) CMSB 2014. LNCS, vol. 8859, pp. 173–195. Springer, Cham (2014). https://doi.org/10.1007/978-3-319-12982-2_13
Kuhn, S., Ulidowski, I.: Towards modelling of local reversibility. In: Krivine, J., Stefani, J.-B. (eds.) RC 2015. LNCS, vol. 9138, pp. 279–284. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-20860-2_19
Kuhn, S., Ulidowski, I.: A calculus for local reversibility. In: Devitt, S., Lanese, I. (eds.) RC 2016. LNCS, vol. 9720, pp. 20–35. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-40578-0_2
Kuhn, S., Ulidowski, I.: Local reversibility in a Calculus of Covalent Bonding. Sci. Comput. Program. 151, 18–47 (2017)
Lanese, I., Mezzina, C.A., Stefani, J.-B.: Controlled reversibility and compensations. In: Glück, R., Yokoyama, T. (eds.) RC 2012. LNCS, vol. 7581, pp. 233–240. Springer, Heidelberg (2013). https://doi.org/10.1007/978-3-642-36315-3_19
Lanese, I., Mezzina, C.A., Tiezzi, F.: Causal-consistent reversibility. Bull. EATCS 114, 122–139 (2014)
Phillips, I., Ulidowski, I., Yuen, S.: A reversible process calculus and the modelling of the ERK signalling pathway. In: Glück, R., Yokoyama, T. (eds.) RC 2012. LNCS, vol. 7581, pp. 218–232. Springer, Heidelberg (2013). https://doi.org/10.1007/978-3-642-36315-3_18
Phillips, I., Ulidowski, I.: Reversing Algebraic Process Calculi. J. Logic Algebraic Program. 73, 70–96 (2007)
Schormann, N., Ricciardi, R., Chattopadhyay, D.: Uracil-DNA glycosylases - structural and functional perspectives on an essential family of DNA repair enzymes. Protein Sci. 23, 1667–1685 (2014)
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Kuhn, S. (2018). Simulation of Base Excision Repair in the Calculus of Covalent Bonding. In: Kari, J., Ulidowski, I. (eds) Reversible Computation. RC 2018. Lecture Notes in Computer Science(), vol 11106. Springer, Cham. https://doi.org/10.1007/978-3-319-99498-7_8
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