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An intermediate level of abstraction for computational systems chemistry

: Andersen, Jakob Lykke; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F.


Philosophical Transactions of the Royal Society of London. Series A 375 (2017), No.2109, Art. 20160354, 10 pp.
ISSN: 0080-4614
ISSN: 0962-8428
ISSN: 1364-503X
ISSN: 0264-3820
ISSN: 1471-2962
Journal Article
Fraunhofer IZI ()
graph grammar; graph transformation; hypergraph; reaction network; rule composition

Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, because precise information on the molecular composition, the dominant reaction chemistry and the conditions for that era are scarce. The exploration of large chemical reaction networks is a central aspect in this endeavour. While quantum chemical methods can accurately predict the structures and reactivities of small molecules, they are not efficient enough to cope with largescale reaction systems. The formalization of chemical reactions as graph grammars provides a generative system, well grounded in category theory, at the right level of abstraction for the analysis of large and complex reaction networks. An extension of the basic formalism into the realm of integer hyperflows allows for the identification of complex reaction patterns, such as autocatalysis, in large reaction networks using optimization techniques. This article is part of the themed issue 'Re-conceptualizing the origins of life'.