Related papers: Characterization of Boolean Networks with Single o…
The multisite phosphorylation-dephosphorylation cycle is a motif repeatedly used in cell signaling. This motif itself can generate a variety of dynamic behaviors like bistability and ultrasensitivity without direct positive feedbacks. In…
We study the target control problem of asynchronous Boolean networks, to identify a set of nodes, the perturbation of which can drive the dynamics of the network from any initial state to the desired steady state (or attractor). We are…
Simple nonlinear dynamical systems with multiple stable stationary states are often taken as models for switchlike biological systems. This paper considers the interaction of multiple such simple multistable systems when they are embedded…
We describe all heteroclinic networks in $\mathbb{R}^4$ made of simple heteroclinic cycles of types $B$ or $C$, with at least one common connecting trajectory. For networks made of cycles of type $B$, we study the stability of the cycles…
The control of biological systems presents interesting applications such as cell reprogramming or drug target identification. A common type of control strategy consists in a set of interventions that, by fixing the values of some variables,…
Boolean networks are popular tools for the exploration of qualitative dynamical properties of biological systems. Several dynamical interpretations have been proposed based on the same logical structure that captures the interactions…
Boolean networks at the critical point have been a matter of debate for many years as, e.g., scaling of number of attractor with system size. Recently it was found that this number scales superpolynomially with system size, contrary to a…
Single trial analyses of ensemble activity in alert animals demonstrate that cortical circuits dynamics evolve through temporal sequences of metastable states. Metastability has been studied for its potential role in sensory coding, memory…
Cellular decision-making (CDM) is a dynamic phenomenon often controlled by regulatory networks defining interactions between genes and transcription factor proteins. Traditional studies have focussed on molecular switches such as positive…
A Boolean network is a finite state discrete time dynamical system. At each step, each variable takes a value from a binary set. The value update rule for each variable is a local function which depends only on a selected subset of…
The multiple futile cycle is a phosphorylation system in which a molecular substrate might be phosphorylated sequentially n times by means of an enzymatic mechanism. The system has been studied mathematically using reaction network theory…
We consider a general class of stochastic networks and ask which network nodes need to be controlled, and how, to stabilize and switch between desired metastable (target) states in terms of the first and second statistical moments of the…
Many discrete models of biological networks rely exclusively on Boolean variables and many tools and theorems are available for analysis of strictly Boolean models. However, multilevel variables are often required to account for threshold…
Boolean networks have been widely used in many areas of science and engineering to represent various dynamical behaviour. In systems biology, they became useful tools to study the dynamical characteristics of large-scale biomolecular…
First, the topological structure of a transition system is studied. Then, two types of transition system (TS) representations of Boolean networks (BNs) and Boolean control networks (BCNs) are investigated. The first kind of representation…
Networks of coupled nonlinear oscillators can display a wide range of emergent behaviours under variation of the strength of the coupling. Network equations for pairs of coupled oscillators where the dynamics of each node is described by…
The dual phosphorylation network provides an essential component of intracellular signaling, affecting the expression of phenotypes and cell metabolism. For particular choices of kinetic parameters, this system exhibits multistationarity, a…
When a fluid comprised of multiple phases or constituents flows through a network, non-linear phenomena such as multiple stable equilibrium states and spontaneous oscillations can occur. Such behavior has been observed or predicted in a…
This Thesis presents research at the boundary between Statistical Physics and Biology. First, we have devised a class of Boolean constraint satisfaction problems (CSP) whose solutions describe the feasible operational states of a chemical…
A model of cellular metabolism due to S. Kauffman is analyzed. It consists of a network of Boolean gates randomly assembled according to a probability distribution. It is shown that the behavior of the network depends very critically on…