Stochastic noise reduction upon complexification: positively correlated birth-death type systems

DOI10.1016/J.JTBI.2014.03.007MaRDI QIDQ2415537zbMATH OpenOpenAlexWikidataFDO

Authors M. Rooman, Jaroslav Albert, Mitia Duerinckx

Publication date 23 May 2019

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1403.3310

zbMATH Keywords

Fano factor decreaseintrinsic noiseItô stochastic differential equationsmaster equationsprotein dimerizationstochasticityvariance reduction

Mathematics Subject Classification ID

Stochastic ordinary differential equations (aspects of stochastic analysis) (60H10) Cell biology (92C37) Biochemistry, molecular biology (92C40)

Abstract: Cell systems consist of a huge number of various molecules that display specific patterns of interactions, which have a determining influence on the cell's functioning. In general, such complexity is seen to increase with the complexity of the organism, with a concomitant increase of the accuracy and specificity of the cellular processes. The question thus arises how the complexification of systems - modeled here by simple interacting birth-death type processes - can lead to a reduction of the noise - described by the variance of the number of molecules. To gain understanding of this issue, we investigated the difference between a single system containing molecules that are produced and degraded, and the same system - with the same average number of molecules - connected to a buffer. We modeled these systems using Ito stochastic differential equations in discrete time, as they allow straightforward analytical developments. In general, when the molecules in the system and the buffer are positively correlated, the variance on the number of molecules in the system is found to decrease compared to the equivalent system without a buffer. Only buffers that are too noisy by themselves tend to increase the noise in the main system. We tested this result on two model cases, in which the system and the buffer contain proteins in their active and inactive state, or protein monomers and homodimers. We found that in the second test case, where the interconversion terms are non-linear in the number of molecules, the noise reduction is much more pronounced; it reaches up to 20% reduction of the Fano factor with the parameter values tested in numerical simulations on an unperturbed birth-death model. We extended our analysis to two arbitrary interconnected systems.

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Cited in

(1)

• Noise-reduction through interaction in gene expression and biochemical reaction processes

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