Mathematics of the genome

DOI10.1007/S10208-016-9316-XMaRDI QIDQ1683737zbMATH OpenOpenAlexFDO

Publication date 1 December 2017

Published in Foundations of Computational Mathematics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1510.00080

gene networks genome dynamics Hopf bifurcation pitchfork bifurcation

Bifurcations of singular points in dynamical systems (37G10) Dynamical systems in biology (37N25) Genetics and epigenetics (92D10)

Abstract: This work gives a mathematical foundation for bifurcation from a stable equilibrium in the genome. We construct idealized dynamics associated with the genome. For this dynamics we investigate the two main bifurcations from a stable equilibrium. Finally, we give a mathematical framework for the Repressilator and the Toggle gene circuits.

Review text

The authors consider a directed network, where each node represents a gene and there is a connection from node \(i\) to node \(j\) if gene \(i\) has some control over gene \(j\). The state of each node is described by a non-negative scalar representing the expression level of the associated gene. Interactions between nodes are assumed to be governed by Hill-type equations of the form \(dy/dt=H(x)-by\), where \(x\) and \(y\) are expression levels, \(b\) is a positive constant and \(H\) is a Hill function. From such a network one derives a general equation \(dx/dt=F(x)\), where \(F:(\mathbb{R}^+)^n\rightarrow \mathbb{R}^n\). The main result consists in showing that if the system is at a stable equilibrium and a parameter is varied (and ``the equilibrium does not leave its basin), the generic ``first bifurcation to occur will be either a supercritical pitchfork or a supercritical Hopf. The authors then give examples in 2- and 3-gene networks.

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