Numerical simulation of piecewise-linear models of gene regulatory networks using complementarity systems

Vincent Acary 1, * Hidde de Jong 2 Bernard Brogliato 1
* Corresponding author
1 BIPOP - Modelling, Simulation, Control and Optimization of Non-Smooth Dynamical Systems
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, INPG - Institut National Polytechnique de Grenoble
2 IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks
LAPM - Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble], Inria Grenoble - Rhône-Alpes, Institut Jean Roget
Abstract : Gene regulatory networks control the response of living cells to changes in their environment. A class of piecewise-linear (PWL) models, which capture the switch-like interactions between genes by means of step functions, has been found useful for describing the dynamics of gene regulatory networks. The step functions lead to discontinuities in the right-hand side of the differential equations. This has motivated extensions of the PWL models based on differential inclusions and Filippov solutions, whose analysis requires sophisticated numerical tools. We present a method for the numerical analysis of one proposed extension, called Aizerman-Pyatnitskii (AP)-extension, by reformulating the PWL models as a mixed complementarity system (MCS). This allows the application of powerful methods developed for this class of nonsmooth dynamical systems, in particular those implemented in the Siconos platform. We also show that under a set of reasonable biological assumptions, putting constraints on the right-hand side of the PWL models, AP-extensions and classical Filippov (F)-extensions are equivalent. This means that the proposed numerical method is valid for a range of different solution concepts. We illustrate the practical interest of our approach through the numerical analysis of three well-known networks developed in the field of synthetic biology.
Complete list of metadatas

Cited literature [68 references]  Display  Hide  Download

https://hal.inria.fr/hal-00924044
Contributor : Vincent Acary <>
Submitted on : Sunday, October 29, 2017 - 4:45:49 PM
Last modification on : Thursday, February 7, 2019 - 5:28:48 PM
Long-term archiving on : Tuesday, January 30, 2018 - 12:16:39 PM

File

VAHJBB.pdf
Files produced by the author(s)

Identifiers

Collections

Citation

Vincent Acary, Hidde de Jong, Bernard Brogliato. Numerical simulation of piecewise-linear models of gene regulatory networks using complementarity systems. Physica D: Nonlinear Phenomena, Elsevier, 2014, 269, pp.103-119. ⟨10.1016/j.physd.2013.11.013⟩. ⟨hal-00924044⟩

Share

Metrics

Record views

793

Files downloads

100