The Interplay of Intrinsic and Extrinsic Bounded Noises in Biomolecular Networks

Giulio Caravagna, Giancarlo Mauri, Alberto d'Onofrio

Research output: Contribution to journalArticle

Abstract

After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i) the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii) a model of enzymatic futile cycle and (iii) a genetic toggle switch. In (ii) and (iii) we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

Original languageEnglish
Article numbere51174
JournalPLoS One
Volume8
Issue number2
DOIs
Publication statusPublished - Feb 21 2013

Fingerprint

Noise
Nonlinear networks
Stochastic models
Random processes
Autocorrelation
Switches
Substrate Cycling
Stochastic Processes
stochastic processes
enzymatic reactions
nonlinear models
autocorrelation

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

The Interplay of Intrinsic and Extrinsic Bounded Noises in Biomolecular Networks. / Caravagna, Giulio; Mauri, Giancarlo; d'Onofrio, Alberto.

In: PLoS One, Vol. 8, No. 2, e51174, 21.02.2013.

Research output: Contribution to journalArticle

Caravagna, Giulio ; Mauri, Giancarlo ; d'Onofrio, Alberto. / The Interplay of Intrinsic and Extrinsic Bounded Noises in Biomolecular Networks. In: PLoS One. 2013 ; Vol. 8, No. 2.
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