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Mathematical modelling of nonlinear dynamics generated from modular interconnections in cellular SOS response system

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Abstract

Nonlinear dynamics in synthetic biology systems, generated as a consequence of interconnections between biological modules, poses challenges to the objective of engineering biological systems with predictable characteristics. Mathematical models, that often provide accurate descriptions of the biological modules in isolation, fail to capture such nonlinearities that arise in the interconnected modules. Without the modelling and quantification of these nonlinearities, systems biology models cannot be predictable or reliable. Hence it become a key area of focus of systems and synthetic biologists. To this end, we analyse the nonlinearities in the SOS response system, a prime cellular network in bacterial cells that functions to repair the DNA damage. It is shown that the dynamics of the modules in the SOS response system differ in isolation and in integration, and substantial variation is observed when more modules are connected. The interdependence among major modules is quantified, which imparts whether the integrated dynamics is an attenuation or amplification of the isolated dynamics. From a synthetic biology perspective, our study contributes to the effective engineering of biological devices from the integration of biological modules in a bottom-up fashion. Meanwhile, it also complements the investigations on the DNA damage repairing mechanism in living cells.

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Acknowledgements

This work was funded by Kerala State Council for Science, Technology and Environment (KSCSTE) (Grant Number No. 124/2015/KSCSTE), Government of Kerala, India. We would also like to acknowledge the facilities provided by the Centre for Excellence in Ayur-Informatics Computer Aided Drug Design (Ai-CADD), University of Kerala.

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  1. Department of Computational Biology and Bioinformatics, University of Kerala, Trivandrum, India

    Silpa Bhaskaran & Achuthsankar S. Nair

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  1. Silpa Bhaskaran
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  2. Achuthsankar S. Nair
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Correspondence to Silpa Bhaskaran.

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Bhaskaran, S., Nair, A.S. Mathematical modelling of nonlinear dynamics generated from modular interconnections in cellular SOS response system. Nonlinear Dyn 93, 643–652 (2018). https://doi.org/10.1007/s11071-018-4215-0

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