Reversibility in Chemical Reactions

In this chapter we give an overview of techniques for the modelling and reasoning about reversibility of systems, including out-of-causal-order reversibility, as it appears in chemical reactions. We consider the autoprotolysis of water reaction, and model it with the Calculus of Covalent Bonding, the Bonding Calculus, and Reversing Petri Nets. This exercise demonstrates that the formalisms, developed for expressing advanced forms of reversibility, are able to model autoprotolysis of water very accurately. Characteristics and expressiveness of the three formalisms are discussed and illustrated.

[1]  Iain C. C. Phillips,et al.  Reversing algebraic process calculi , 2007, J. Log. Algebraic Methods Program..

[2]  Irek Ulidowski,et al.  Reversibility and Asymmetric Conflict in Event Structures , 2013, CONCUR.

[3]  Ivan Lanese,et al.  Controlled Reversibility and Compensations , 2012, RC.

[4]  Anna Philippou,et al.  Controlling Reversibility in Reversing Petri Nets with Application to Wireless Communications , 2019, RC.

[5]  Monika Heiner,et al.  Steady state analysis of metabolic pathways using Petri nets , 2003, Silico Biol..

[6]  Irek Ulidowski,et al.  A Calculus for Local Reversibility , 2016, RC.

[7]  Russ B. Altman,et al.  Research Paper: Using Petri Net Tools to Study Properties and Dynamics of Biological Systems , 2004, J. Am. Medical Informatics Assoc..

[8]  Stefan Kuhn.  Simulation of Base Excision Repair in the Calculus of Covalent Bonding , 2018, RC.

[9]  Marta Simeoni,et al.  Petri nets for modelling metabolic pathways: a survey , 2010, Natural Computing.

[10]  Michael L. Mavrovouniotis,et al.  Petri Net Representations in Metabolic Pathways , 1993, ISMB.

[11]  Irek Ulidowski,et al.  Modelling of Bonding with Processes and Events , 2013, RC.

[12]  Luca Cardelli,et al.  BioAmbients: an abstraction for biological compartments , 2004, Theor. Comput. Sci..

[13]  Irek Ulidowski,et al.  Local reversibility in a Calculus of Covalent Bonding , 2018, Sci. Comput. Program..

[14]  Irek Ulidowski,et al.  A Reversible Process Calculus and the Modelling of the ERK Signalling Pathway , 2012, RC.

[15]  Wan Fokkink,et al.  Introduction to Process Algebra , 1999, Texts in Theoretical Computer Science. An EATCS Series.

[16]  Corrado Priami,et al.  Beta Binders for Biological Interactions , 2004, CMSB.

[17]  Masao Nagasaki,et al.  Hybrid Petri net based modeling for biological pathway simulation , 2011, Natural Computing.

[18]  Robin Milner,et al.  A Calculus of Communicating Systems , 1980, Lecture Notes in Computer Science.

[19]  Lukasz Mikulski,et al.  Reversing Computations Modelled by Coloured Petri Nets , 2018, ATAED@Petri Nets/ACSD.

[20]  François Fages,et al.  Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM , 2002 .

[21]  Aviv Regev,et al.  The π-calculus as an Abstraction for Biomolecular Systems , 2004 .

[22]  Irek Ulidowski,et al.  Equivalences on observable processes , 1992, [1992] Proceedings of the Seventh Annual IEEE Symposium on Logic in Computer Science.

[23]  Corrado Priami,et al.  Stochastic pi-Calculus , 1995, Comput. J..

[24]  Vincent Danos,et al.  Reversible Communicating Systems , 2004, CONCUR.

[25]  Ivan Lanese,et al.  Reversing Higher-Order Pi , 2010, CONCUR.

[26]  Wolfgang Reisig,et al.  Understanding Petri nets , 1995, IEEE Parallel & Distributed Technology: Systems & Applications.

[27]  Wolfgang Reisig,et al.  Understanding Petri Nets Modeling Techniques, Analysis Methods, Case Studies , 2013, Bull. EATCS.

[28]  Ina Koch.  Petri nets in systems biology , 2014, Software & Systems Modeling.

[29]  Louchka Popova-Zeugmann,et al.  Time Petri Nets for Modelling and Analysis of Biochemical Networks , 2005, Fundam. Informaticae.

[30]  R Hofestädt,et al.  Quantitative modeling of biochemical networks , 1998, Silico Biol..

[31]  Irek Ulidowski,et al.  Reversing Event Structures , 2018, New Generation Computing.

[32]  Claudine Chaouiya,et al.  Petri net modelling of biological networks , 2007, Briefings Bioinform..

[33]  Jane Hillston,et al.  Bio-PEPA: A framework for the modelling and analysis of biological systems , 2009, Theor. Comput. Sci..

[34]  Ivan Lanese,et al.  Controlling Reversibility in Higher-Order Pi , 2011, CONCUR.

[35]  Vincent Danos,et al.  Rule-Based Modelling of Cellular Signalling , 2007, CONCUR.

[36]  James R Faeder,et al.  Rule-based modeling of biochemical systems with BioNetGen. , 2009, Methods in molecular biology.

[37]  Anna Philippou,et al.  Reversible Computation in Petri Nets , 2018, RC.