In this study, I have studied extensively the ability of the double toggle switch pattern to implement memory in gene regulatory networks. I have implemented computationally an ecologically realist model of the pattern, introducted a discretised model of its functional dynamics, and showed that the absence of scale separation between functional dynamics and expression noise in ecological settings did not constrain the system's ability to discriminate information and retain it through time. Further study could deepen the discretised model I have introduced, for exemple by investigating whether a discretised scale exists where the system can be modelled as Markovian.
Bibliography
Barabasi et al, 2003
Barabàsi, Albert-Làsilò, and Eric Bonabeau. 2003. ‘Scale-Free Networks’. Scientific American 288(5): 60–69.
Larremore et al, 2011
Larremore, Daniel B., Woodrow L. Shew, and Juan G. Restrepo. 2011. ‘Predicting Criticality and Dynamic Range in Complex Networks: Effects of Topology’. Physical Review Letters 106(5): 058101.
Fronczak et al, 2006
Fronczak, Piotr, Agata Fronczak, and Janusz A. Hołyst. 2006. ‘Self-Organized Criticality and Coevolution of Network Structure and Dynamics’. Physical Review E 73(4): 046117.
Massobrio et al, 2015
Massobrio, Paolo, Valentina Pasquale, and Sergio Martinoia. 2015. ‘Self-Organized Criticality in Cortical Assemblies Occurs in Concurrent Scale-Free and Small-World Networks’. Scientific Reports 5(1): 10578.
Migliano et al, 2020
Migliano, Andrea B. et al. 2020. ‘Hunter-Gatherer Multilevel Sociality Accelerates Cumulative Cultural Evolution’. Science Advances 6(9): eaax5913.
Chialvo et al, 2010
Chialvo, Dante R. 2010. ‘Emergent Complex Neural Dynamics’. Nature Physics 6(10): 744–50.
Friston et al, 2012
Karl, Friston. 2012. ‘A Free Energy Principle for Biological Systems’. Entropy 14(11): 2100–2121.
Milo et al, 2002
Milo, R. et al. 2002. ‘Network Motifs: Simple Building Blocks of Complex Networks’. Science 298(5594): 824–27.
Herbach et al, 2017
Herbach, Ulysse, Arnaud Bonnaffoux, Thibault Espinasse, and Olivier Gandrillon. 2017. ‘Inferring Gene Regulatory Networks from Single-Cell Data: A Mechanistic Approach’. BMC Systems Biology 11(1): 105.
Gillespie, 1976
Gillespie, Daniel. 1976. ‘A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reaction’. Journal of Computational Physics 22: 403–34.
Viñuelas et al, 2013
Viñuelas, José et al. 2013. ‘Quantifying the Contribution of Chromatin Dynamics to Stochastic Gene Expression Reveals Long, Locus-Dependent Periods between Transcriptional Bursts’. BMC Biology 11(1): 15.