Coping with dynamical reaction system topologies using deterministic P modules: a case study of photosynthesis
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Coping with dynamical reaction system topologies using deterministic P modules: a case study of photosynthesis Thomas Hinze1 Received: 12 June 2020 / Accepted: 6 October 2020 © The Author(s) 2020
Abstract The topology of chemical reaction networks is commonly treated as a static structure. This might be sufficient if substrate concentrations and kinetic parameter values exclusively determine the behaviour of all considered reactions. In contrast, numerous phenomena observed in life sciences imply a different nature by dynamical composition of reaction schemes. Single reactions or functional groups of reactions (modules) become activated or deactivated by external signals such as light intensity while the system is in operation. In other scenarios, reactions emerge or disappear while modules can connect to each other or disconnect due to presence or absence of corresponding trigger signals. We capture dynamical reaction network structures by an extended version of deterministic P modules with evaluation of trigger signals which facilitates detailed in-silico simulation studies and hence an easier understanding and prediction of complex biological systems. A case study dedicated to photosynthesis in plants demonstrates its usefulness beyond pure employment of ordinary differential equations by consideration of events, non-differentiable external trigger signals, and thresholds which collaterally modify the underlying reaction scheme. Keywords Deterministic P module · Dynamical reaction system · Activate and deactivate reactions by trigger signals · Photosynthesis · Simulation case study
1 Introduction Chemical reaction schemes, particularly those found in living organisms, appear to represent invisible networks. Identification of individual reactions mainly results from observation of measurable molecular interactions which reveals potentially involved substrates on the one hand and catalysts as well as products on the other hand [17]. Whenever specific substances seem to be related to each other within a couple of reproducible experiments, it is assumed that there exists a chemical reaction. Fluorescence markers attached to substances under study in concert with highly developed screening techniques and manifold fine-grained weighing, tests, and visualisations can substantiate hypotheses towards proved assumptions. This comes along with a growing knowledge about single reactions, pathways, and finally entire reaction schemes suitable to fulfil certain * Thomas Hinze thomas.hinze@uni‑jena.de 1
Friedrich Schiller University Jena, Ernst‑Abbe‑Platz 2, 07743 Jena, Germany
tasks. Comprehensive collections and repositories of reaction schemes have been reported up to now [15, 26]. Most of them concern aspects of metabolism, cell signalling, or gene expression [5]. When retrieving public data bases, it stands out that reaction schemes are commonly managed in a static manner. The topology of a reaction network is typically represented by an invariable, inherently unmodifiable structure. For small and
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