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2022 | OriginalPaper | Buchkapitel

Abstraction-Based Segmental Simulation of Chemical Reaction Networks

verfasst von : Martin Helfrich, Milan Češka, Jan Křetínský, Štefan Martiček

Erschienen in: Computational Methods in Systems Biology

Verlag: Springer International Publishing

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Abstract

Simulating chemical reaction networks is often computationally demanding, in particular due to stiffness. We propose a novel simulation scheme where long runs are not simulated as a whole but assembled from shorter precomputed segments of simulation runs. On the one hand, this speeds up the simulation process to obtain multiple runs since we can reuse the segments. On the other hand, questions on diversity and genuineness of our runs arise. However, we ensure that we generate runs close to their true distribution by generating an appropriate abstraction of the original system and utilizing it in the simulation process. Interestingly, as a by-product, we also obtain a yet more efficient simulation scheme, yielding runs over the system’s abstraction. These provide a very faithful approximation of concrete runs on the desired level of granularity, at a low cost. Our experiments demonstrate the speedups in the simulations while preserving key dynamical as well as quantitative properties.

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Vorheriges Kapitel Abstract Simulation of Reaction Networks via Boolean Networks

Nächstes Kapitel Qualitative Dynamics of Chemical Reaction Networks: An Investigation Using Partial Tropical Equilibrations

We can handle alternative kinetics including Michaelis-Menten and Hill kinetics.

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Titel: Abstraction-Based Segmental Simulation of Chemical Reaction Networks
verfasst von: Martin Helfrich
Milan Češka
Jan Křetínský
Štefan Martiček
Verlag: Springer International Publishing
Buch: Computational Methods in Systems Biology
Print ISBN: 978-3-031-15033-3

Electronic ISBN: 978-3-031-15034-0

Copyright-Jahr: 2022
DOI: https://doi.org/10.1007/978-3-031-15034-0_3

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