Related papers: Biochemical Oscillations in Delayed Negative Cycli…
Sensitivity analysis is a classical and fundamental tool to evaluate the role of a given parameter in a given system characteristic. Because the phase response curve is a fundamental input--output characteristic of oscillators, we developed…
Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules…
Understanding relationship between noisy dynamics and biological network architecture is a fundamentally important question, particularly in order to elucidate how cells encode and process information. We analytically and numerically…
Biological oscillators are very diverse but can be classified based on dynamical motifs such as the types of feedback loops present. The S. Elongatus circadian clock is a remarkable phosphorylation-based oscillator that can be reconstituted…
The Duffing oscillator is a nonlinear extension of the ubiquitous harmonic oscillator and as such plays an outstanding role in science and technology. Experimentally, the system parameters are determined by a measurement of its response to…
Biological oscillators coordinate individual cellular components so that they function coherently and collectively. They are typically composed of multiple feedback loops, and period mismatch is unavoidable in biological implementations. We…
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
Genetic oscillators play important roles in cell life regulation. The regulatory efficiency usually depends strongly on the emergence of stable collective dynamic modes, which requires designing the interactions between genetic networks. We…
Chaotic oscillators have gained significant attention in the research community because of their ability to reproduce and investigate the complex dynamics of real-world phenomena. Recent advances in the design of chaotic oscillator…
We study the effects of multiple binding sites in the promoter of a genetic oscillator. We evaluate the regulatory function of a promoter with multiple binding sites in the absence of cooperative binding, and consider different hypotheses…
Common models of circadian rhythms are constructed as compartmental reactions of well mixed biochemicals involving a negative-feedback loop containing several intermediate reaction steps in order to enable oscillations. Spatial transport of…
Auto-regulation, a process wherein a protein negatively regulates its own production, is a common motif in gene expression networks. Negative feedback in gene expression plays a critical role in buffering intracellular fluctuations in…
The study of synchronization among genetic oscillators is essential for the understanding of the rhythmic phenomena of living organisms at both molecular and cellular levels. Genetic networks are intrinsically noisy due to natural random…
Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse…
Networks of globally coupled, noise activated, bistable elements with connection time delays are considered. The dynamics of these systems is studied numerically using a Langevin description and analytically using (1) a Gaussian…
Living systems regulate many aspects of their behavior through periodic oscillations of molecular concentrations, which function as `biochemical clocks.' These clocks are intrinsically subject to thermal fluctuations, so that the duration…
We report the splitting of an oscillating DNA circuit into $\sim 700$ droplets with picoliter volumes. Upon incubation at constant temperature, the droplets display sustained oscillations that can be observed for more than a day.…
Oscillator networks found in social and biological systems are characterized by the presence of wide ranges of coupling strengths and complex organization. Yet robustness and synchronization of oscillations are found to emerge on…
We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their…
A self-regulatory genetic circuit, where a protein acts as a positive regulator of its own production, is known to be a simplest form of biological network with a positive feedback loop. Although at least three components, DNA, RNA, and the…