Related papers: Oscillations in three-reaction quadratic mass-acti…
We address the question of which small, bimolecular, mass action chemical reaction networks (CRNs) are capable of Andronov-Hopf bifurcation (from here on abbreviated to "Hopf bifurcation"). It is easily shown that any such network must have…
In this paper we study bifurcations in mass-action networks with two chemical species and reactant complexes of molecularity no more than two. We refer to these as planar, quadratic networks as they give rise to (at most) quadratic…
We present a three-dimensional differential equation, which robustly displays a degenerate Andronov-Hopf bifurcation of infinite codimension, leading to a center, i.e., an invariant two-dimensional surface that is filled with periodic…
We present some simple mass-action systems with limit cycles that fall under the scope of the Deficiency-One Theorem. All the constructed examples are mass-conserving and their stoichiometric subspace is two-dimensional. Using the…
Phosphorylation networks, representing the mechanisms by which proteins are phosphorylated at one or multiple sites, are ubiquitous in cell signalling and display rich dynamics such as unlimited multistability. Dual-site phosphorylation…
Autonomous sustained oscillations are ubiquitous in living and nonliving systems. As open systems, far from thermodynamic equilibrium, they defy entropic laws which mandate convergence to stationarity. We present structural conditions on…
Experimental evidence suggests that the computational state of cortical systems change according to behavioral and stimulus context. However, it is still unknown what mechanisms underlie this adaptive processing in cortical circuitry. In…
For the reaction networks with zero-one stoichiometric coefficients (or simply zero-one networks), we prove that if a network admits a Hopf bifurcation, then the rank of the stoichiometric matrix is at least four. As a corollary, we show…
We discuss three examples of bimolecular mass-action systems with three species, due to Feinberg, Berner, Heinrich, and Wilhelm. Each system has a unique positive equilibrium which is unstable for certain rate constants and then exhibits…
Reaction networks taken with mass-action kinetics arise in many settings, from epidemiology to population biology to systems of chemical reactions. Bistable reaction networks are posited to underlie biochemical switches, which motivates the…
Reaction networks have been widely used as generic models in diverse areas of applied sciences, such as biology, chemistry, ecology, epidemiology, and computer science. A reaction network incorporating noisy effects is modeled as a…
We state two sufficient criteria for periodic oscillations in mass action systems. Neither criterion requires a computation of the Hurwitz determinants. Instead, both criteria exploit the linear algebra concepts of $D$-stability and…
We demonstrate that strongly asymmetric limit cycles can be observed in the system of three identical ring oscillators (3-gene networks known as Repressilators) globally coupled by signal molecule diffusion added to the model in a way like…
Oscillation has an important role in bio-dynamical systems such as circadian rhythms and eukaryotic cell cycle. John Tyson et. al. in Nature Review Mol Cell Biol 2008 examined a limited number of network topologies consisting of three nodes…
We consider the macroscopic regimes and the scenarios for the onset and the suppression of collective oscillations in a heterogeneous population of active rotators, comprised of excitable or oscillatory elements. We analyze the system in…
One- and two-parameter families of flows in $R^3$ near an Andronov-Hopf bifurcation (AHB) are investigated in this work. We identify conditions on the global vector field, which yield a rich family of multimodal orbits passing close to a…
Double Hopf bifurcation analysis can be used to reveal some complicated dynamical behavior in a dynamical system, such as the existence or coexistence of periodic orbits, quasi-periodic orbits, or even chaos. In this paper, an algorithm for…
We analyze a family of clustered excitatory-inhibitory neural networks and the underlying bifurcation structures that arise because of permutation symmetries in the network as the global coupling strength $g$ is varied. We primarily…
Chemical reaction systems are dynamical systems that arise in chemical engineering and systems biology. In this work, we consider the question of whether the minimal (in a precise sense) multistationary chemical reaction networks, which we…
This work investigates the emergence of oscillations in one of the simplest cellular signaling networks exhibiting oscillations, namely, the dual-site phosphorylation and dephosphorylation network (futile cycle), in which the mechanism for…