Related papers: Oscillation patterns in negative feedback loops
Inside individual cells, expression of genes is stochastic across organisms ranging from bacterial to human cells. A ubiquitous feature of stochastic expression is burst-like synthesis of gene products, which drives considerable…
We study the interplay between noise and a positive feedback mechanism in an excitable system that generates events. We show that such a system can exhibit a bistability in the dynamics of the event generation (states of low and high…
Systems with the coexistence of different stable attractors are widely exploited in systems biology in order to suitably model the differentiating processes arising in living cells. In order to describe genetic regulatory networks several…
The protein p53 has a well established role in protecting genomic integrity in human cells. When DNA is damaged p53 induces the cell cycle arrest to prevent the transmission of the damage to cell progeny, triggers the production of proteins…
Positive feedback regulation is ubiquitous in cell signaling networks, often leading to binary outcomes in response to graded stimuli. However, the role of such feedbacks in clustering, and in spatial spreading of activated molecules, has…
Understanding the oscillating behaviors that govern organisms' internal biological processes requires interdisciplinary efforts combining both biological and computer experiments, as the latter can complement the former by simulating…
Cell phenotype dynamic homeostasis contrasts with the inherent randomness of intracellular reactions. Although feedback control of master regulatory genes (MRG) is a key strategy for maintaining gene network expression ranges limited,…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
Coupled oscillator networks show a complex interrelations between topological characteristics of the network and the nonlinear stability of single nodes with respect to large but realistic perturbations. We extend previous results on these…
Neural oscillations are universal phenomena and can be observed at different levels of neural systems, from single neuron to macroscopic brain. The frequency of those oscillations are related to the brain functions. However, little is know…
Whereas the positive equilibrium of a mass-action system with deficiency zero is always globally stable, for deficiency-one networks there are many different scenarios, mainly involving oscillatory behaviour. We present several examples,…
A minimalistic model of the half-center oscillator is proposed. Within it, we consider dynamics of two excitable neurons interacting by means of the excitatory coupling. In the parameter space of the model, we identify the regions of…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
Genes are connected in regulatory networks, often modelled by ordinary differential equations. Changes in expression of a gene propagate to other genes along paths in the network. At a stable state, the system's Jacobian matrix confers…
Circadian clocks are biochemical oscillators that allow organisms to estimate the time of the day. These oscillators are inherently noisy due to the discrete nature of the reactants and the stochastic character of their interactions. To…
The global dynamics of gene regulatory networks are known to show robustness to perturbations in the form of intrinsic and extrinsic noise, as well as mutations of individual genes. One molecular mechanism underlying this robustness has…
A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…
Stochastic processes are commonly used models to describe dynamics of a wide variety of nonequilibrium phenomena ranging from electrical transport to biological motion. The transition matrix describing a stochastic process can be regarded…
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…
This note addresses the output synchronization problem of incrementally output-feedback passive nonlinear systems in the presence of exogenous disturbances. Two kinds of distributed controllers are proposed; one placed at the nodes and the…