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2022 | OriginalPaper | Chapter

Algebraic Biochemistry: A Framework for Analog Online Computation in Cells

Authors : Mathieu Hemery, François Fages

Published in: Computational Methods in Systems Biology

Publisher: Springer International Publishing

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Abstract

The Turing completeness of continuous chemical reaction networks (CRNs) states that any computable real function can be computed by a continuous CRN on a finite set of molecular species, possibly restricted to elementary reactions, i.e. with at most two reactants and mass action law kinetics. In this paper, we introduce a notion of online analog computation for the CRNs that stabilize the concentration of their output species to the result of some function of the concentration values of their input species, whatever changes are operated on the inputs during the computation. We prove that the set of real functions stabilized by a CRN with mass action law kinetics is precisely the set of real algebraic functions.

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next chapter Abstract Simulation of Reaction Networks via Boolean Networks

All the computational results presented in this paper are available in an executable Biocham notebook at https://lifeware.inria.fr/wiki/Main/Software#CMSB22.

The terminology of “algebraic functions” used in the title of [1] refers in fact to its restriction to algebraic expressions.

An Ubuntu 20.04, with an Intel Core i6, 2.4 GHz x 4 cores and 15.5 GB of memory.

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Title: Algebraic Biochemistry: A Framework for Analog Online Computation in Cells
Authors: Mathieu Hemery
François Fages
Publisher: Springer International Publishing
Book: Computational Methods in Systems Biology
Print ISBN: 978-3-031-15033-3

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

Copyright Year: 2022
DOI: https://doi.org/10.1007/978-3-031-15034-0_1

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