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Bounded noises as a natural tool to model extrinsic fluctuations in biomolecular networks

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Abstract

In the first part of this invited paper we review the role of both extrinsic and intrinsic stochasticity in shaping the dynamics of biomolecular networks. In particular, we stress the use of bounded stochastic processes as a model of extrinsic random perturbations. In the second part, we propose three examples of molecular circuits under the influence of external fluctuations modeled by means of bounded noises. The first two examples involve the linear decay of a protein with, respectively, large or low number of molecules, so to stress different modeling approaches. The third example concerns the spatio-temporal dynamics of proteins determining the chemotaxis-driven polarization of a cell. In these examples one can observe phenomena that are dependent on the specific class of employed bounded noise.

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Acknowledgments

The authors would like to thank the anonymous referees for invaluable comments which improved the paper. AdO wishes to thank the organizers of Wivace (Italian Workshop on Artificial Life and Evolutionary Computation) for the invitation to present these topics to the 2013 edition of the workshop and in this special issue.

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  1. Alberto d’Onofrio

    Present address: International Prevention Research Institute, 15 Chemin du Saquin, Ecully, 69130, Lyon, France

Authors and Affiliations

  1. Department of Experimental Oncology, European Institute of Oncology, Via Ripamonti 435, 20141, Milano, Italy

    Sebastiano de Franciscis & Alberto d’Onofrio

  2. Universitá degli Studi di Milano-Bicocca, Dipartimento di Informatica, Sistemistica e Comunicazione, Viale Sarca 336, 20126, Milano, Italy

    Giulio Caravagna

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  1. Sebastiano de Franciscis
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Correspondence to Alberto d’Onofrio.

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The research of A. d’Onofrio and S. de Franciscis has been done in the framework of the Integrated Project “P-medicine—from data sharing and integration via VPH models to personalized medicine” (Project ID: 270089), which is partially funded by the European Commission under the 7th framework program.

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de Franciscis, S., Caravagna, G. & d’Onofrio, A. Bounded noises as a natural tool to model extrinsic fluctuations in biomolecular networks. Nat Comput 13, 297–307 (2014). https://doi.org/10.1007/s11047-014-9424-y

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