Reducing the complexity of mathematical models for the plant circadian clock by distributed delays

Abstract

A major bottleneck in the modelling of biological networks is the parameter explosion problem - the exponential increase in the number of parameters that need to be optimised to data as the size of the model increases. Here, we address this problem in the context of the plant circadian clock by applying the method of distributed delays. We show that using this approach, the system architecture can be simplified efficiently - reducing the number of parameters - whilst still preserving the core mechanistic dynamics of the gene regulatory network. Compared to models with discrete time-delays, which are governed by functional differential equations, the distributed delay models can be converted into sets of equivalent ordinary differential equations, enabling the use of standard methods for numerical integration, and for stability and bifurcation analyses. We demonstrate the efficiency of our modelling approach by applying it to three exemplar mathematical models of the Arabidopsis circadian clock of varying complexity, obtaining significant reductions in complexity in each case. Moreover, we revise one of the most up-to-date Arabidopsis models, updating the regulation of the PRR9 and PRR7 genes by LHY in accordance with recent experimental data. The revised model more accurately reproduces the LHY-induction experiments of core clock genes, compared with the original model. Our work thus shows that the method of distributed delays facilitates the optimisation and reformulation of genetic network models.

Keywords: Arabidopsis thaliana; Computational modelling; Distributed delays; Parameter optimisation; Plant circadian clock; Systems biology.