Related papers: Robustness of clocks to input noise
Living organisms need to be sensitive to a changing environment while also ignoring uninformative environmental fluctuations. Here, we show that the circadian clock in \textit{Synechococcus elongatus} can naturally tune its environmental…
Circadian oscillation provides selection advantages through synchronization to the daylight cycle. However, a reliable clock must be designed through two conflicting properties: entrainability to synchronize internal time with periodic…
A fundamental description of time can be consistent not only with the usual monotonic behavior but also with a periodic physical clock variable, coupled to the degrees of freedom of a system evolving in time. Generically, one would in fact…
Overdamped stochastic systems maintained far from equilibrium can display sustained oscillations with fluctuations that decrease with the system size. The correlation time of such noisy limit cycles expressed in units of the cycle period is…
Circadian clocks are oscillatory genetic networks that help organisms adapt to the 24-hour day/night cycle. The clock of the green alga Ostreococcus tauri is the simplest plant clock discovered so far. Its many advantages as an experimental…
The effect of small-amplitude noise on excitable systems with large time-scale separation is analyzed. It is found that small random perturbations of the fast excitatory variable result in the onset of a quasi-deterministic limit cycle…
Nearly all living organisms, including some bacterial species, exhibit biological processes with a period of about 24 h called circadian (from the Latin circa, about, dies, day) rhythms. These rhythms allow living organisms to anticipate…
Long and stable timescales are often observed in complex biochemical networks, such as in emergent oscillations. How these robust dynamics persist remains unclear, given the many stochastic reactions and shorter time scales demonstrated by…
Being able to measure time, whether directly or indirectly, is a significant advantage for an organism. It allows for the timely reaction to regular or predicted events, reducing the pressure for fast processing of sensory input. Thus,…
All clocks, classical or quantum, are open non equilibrium irreversible systems subject to the constraints of thermodynamics. Using examples I show that these constraints necessarily limit the performance of clocks and that good clocks…
Circadian clocks must be able to entrain to time-varying signals to keep their oscillations in phase with the day-night rhythm. On the other hand, they must also exhibit input compensation: their period must remain about one day in…
Daylight plays a major role in the wake/sleep cycle in humans. Indeed, the wake/sleep system stems from biological systems that follow a circadian rhythm determined by the light/dark alternation. The oscillations can be modeled by the…
Stuart-Landau limit-cycle oscillators are a paradigm in the study of coherent and incoherent limit cycles. In this work, we generalize the standard Stuart-Landau dimer model to include effects due to an inertia-like term and noise and study…
Oscillations in nonequilibrium noisy systems are important physical phenomena. These oscillations can happen in autonomous biochemical oscillators such as circadian clocks. They can also manifest as subharmonic oscillations in periodically…
Automated verification of living organism models allows us to gain previously unknown knowledge about underlying biological processes. In this paper, we show the benefits to use parametric time Petri nets in order to analyze precisely the…
We consider a periodic quantum clock based on cooperative resonance fluorescence at zero temperature. In the quantum case, this system has an exact steady state and the limit cycle appears in conditional quantum dynamics under homodyne…
Recent measurements of durations of non-equilibrium processes provide valuable information on microscopic mechanisms and energetics. Comprehensive theory for corresponding experiments so far is well developed for single-particle systems…
The effects of noise on the dynamics of nonlinear systems is known to lead to many counter-intuitive behaviors. Using simple planar limit cycle oscillators, we show that the addition of moderate noise leads to qualitatively different…
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 develop an abstract model of atomic clocks that fully describes the dynamics of repeated synchronization between a classical oscillator and a quantum reference. We prove existence of a stationary state of the model and study its…