Nets with mana: a framework for chemical reaction modelling

DOI10.1007/978-3-030-78946-6_10zbMATH Open1492.68095arXiv2101.06234OpenAlexW3175798954MaRDI QIDQ2117265FDOQ2117265

Authors: Fabrizio Genovese, Daniele Palombi, Fosco Loregiàn 

Publication date: 21 March 2022

Abstract: We use categorical methods to define a new flavor of Petri nets where transitions can only fire a limited number of times, specified by a quantity that we call mana. We do so with chemistry in mind, looking at ways of modelling the behavior of chemical reactions that depend on enzymes to work. We prove that such nets can be either obtained as a result of a comonadic construction, or by enriching them with extra information encoded into a functor. We then use a well-established categorical result to prove that the two constructions are equivalent, and generalize them to the case where the firing of some transitions can "regenerate" the mana of others. This allows us to represent the action of catalysts and also of biochemical processes where the byproducts of some chemical reaction are exactly the enzymes that another reaction needs to work.

Full work available at URL: https://arxiv.org/abs/2101.06234

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Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Monads (= standard construction, triple or triad), algebras for monads, homology and derived functors for monads (18C15) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85) Classical flows, reactions, etc. in chemistry (92E20) Monoidal categories, symmetric monoidal categories (18M05)

Cites Work

• Monoidal functors, species and Hopf algebras
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• Introduction to bicategories
• Organizational invariance and metabolic closure: analysis in terms of \((M, R)\) systems
• Petri nets are monoids
• The span construction
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• On the category of Petri net computations
• (Co)end Calculus
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• Universal Petri net
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Cited In (3)

• A categorical semantics for hierarchical Petri nets
• Network models from Petri nets with catalysts
• A compositional framework for reaction networks

Uses Software

• idris-ct

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