Related papers: Bifurcation of Transition Paths Induced by Coupled…
We study the versatile performance of networks of coupled circuits. Each of these circuits is composed of a positive and a negative feedback loop in a motif that is frequently found in genetic and neural networks. When two of these circuits…
We show how coupling an ensemble of bistable systems to a common cavity field affects the collective stochastic behavior of this ensemble. In particular, the cavity provides an effective interaction between the systems, and parametrically…
Bifurcations in a system of coupled maps are investigated. Using symbolic dynamics it is proven that for coupled shift maps the well known space--time--mixing attractor becomes unstable at a critical coupling strength in favour of a…
We explore the connection between a stochastic simulation model and an ordinary differential equations (ODEs) model of the dynamics of an excitable gene circuit that exhibits noise-induced oscillations. Near a bifurcation point in the ODE…
Various biological phenomena, like cell differentiation and pattern formation in multicellular organisms, are explained using the bifurcation theory. Molecular network motifs like positive feedback and mutual repressor exhibit bifurcation…
Sudden and abrupt changes can occur in a nonlinear system within many fields of science when such a system crosses a tipping point and rapid changes of the system occur in response to slow changes in an external forcing. These can occur…
We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address this nonlinearity we introduce a general perturbative methodology based on assuming timescale separation between noise and genes dynamics, with…
We investigate the emergence of complex dynamics in a system of coupled dissipative kicked rotors and show that critical transitions can be understood via bifurcations of simple states. We study multistability and bifurcations in the single…
We present a path - integral approach to treat a 2D model of a quantum bifurcation. The model potential has two equivalent minima separated by one or two saddle points, depending on the value of a continuous parameter. Tunneling is…
Ordinary differential equations (ODEs) can model the transition of cell states over time. Bifurcation theory is a branch of dynamical systems which studies changes in the behavior of an ODE system while one or more parameters are varied. We…
Living cells need a constant availability of certain resources to have a sustained gene expression process. Limited availability of cellular resources for gene expression, like ribosomes, along with a variation of resource affinity,…
A celebrated result in bifurcation theory is that global connected sets of non-trivial solutions bifurcate from trivial solutions at non-zero eigenvalues of odd algebraic multiplicity of the linearized problem when the operators involved…
Genetic switch systems with mutual repression of two transcription factors are studied using deterministic methods (rate equations) and stochastic methods (the master equation and Monte Carlo simulations). These systems exhibit bistability,…
We study a system of dynamical units, each of which shows excitable or oscillatory behavior, depending on the choice of parameters. When we couple these units with repressive bonds, we can control the duration of collective oscillations for…
Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because…
We present an analytical treatment of a genetic switch model consisting of two mutually inhibiting genes operating without cooperative binding of the corresponding transcription factors. Previous studies have numerically shown that these…
A variation in the environment of a system, such as the temperature, the concentration of a chemical solution or the appearance of a magnetic field, may lead to a drift in one of the parameters. If the parameter crosses a bifurcation point,…
We study a system of coupled phase oscillators near a saddle-node on an invariant circle bifurcation and driven by random intrinsic frequencies. Under the variation of control parameters, the system undergoes a phase transition changing the…
We present a detailed dynamical model of the behavior of transcription-translation circuits in vitro that makes explicit the roles played by essential molecular resources. A set of simple two-gene test circuits operating in a cell-free…
A boundary equilibrium bifurcation (BEB) in a hybrid dynamical system occurs when a regular equilibrium collides with a switching surface in phase space. This causes a transition to a pseudo-equilibrium embedded within the switching…