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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…

Biological Physics · Physics 2018-03-21 Michele Monti , David K. Lubensky , Pieter Rein ten Wolde

To estimate the time, many organisms, ranging from cyanobacteria to animals, employ a circadian clock which is based on a limit-cycle oscillator that can tick autonomously with a nearly 24h period. Yet, a limit-cycle oscillator is not…

Molecular Networks · Quantitative Biology 2018-08-22 Michele Monti , David K Lubensky , Pieter Rein ten Wolde

Circadian clocks are the central timekeepers of life, allowing cells to anticipate changes between day and night. Experiments in recent years have revealed that circadian clocks can be highly stable, raising the question how reliably they…

Molecular Networks · Quantitative Biology 2016-06-22 Michele Monti , Pieter Rein ten Wolde

Continuous clocks, i.e. the clocks that measure time in a continuous manner, are regarded as an essential component of sensing technology. Precision and recurrence time are two basic features of continuous clocks. In this paper, in the…

Quantum Physics · Physics 2022-09-02 Mehdi Ramezani , Morteza Nikaeen , Alireza Bahrampour

The circadian clocks keeping time of day in many living organisms rely on self-sustained biochemical oscillations which can be entrained by external cues, such as light, to the 24-hour cycle induced by Earth rotation. However, environmental…

Quantitative Methods · Quantitative Biology 2015-05-20 Benjamin Pfeuty , Quentin Thommen , Marc Lefranc

We have re-analyzed the stability of pulse arrival times from pulsars and white dwarfs using several analysis tools for measuring the noise characteristics of sampled time and frequency data. We show that the best terrestrial artificial…

Instrumentation and Methods for Astrophysics · Physics 2011-01-12 John G. Hartnett , Andre Luiten

The circadian clock is an internal timer that coordinates the daily rhythms of behavior and physiology, including sleep and hormone secretion. Accurately tracking the state of the circadian clock, or circadian phase, holds immense potential…

Dynamical Systems · Mathematics 2023-06-14 Dae Wook Kim , Minki P. Lee , Daniel B. Forger

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,…

Other Quantitative Biology · Quantitative Biology 2019-06-19 Andrei D. Robu , Christoph Salge , Chrystopher L. Nehaniv , Daniel Polani

An efficient estimator is constructed for the quadratic covariation or integrated co-volatility matrix of a multivariate continuous martingale based on noisy and nonsynchronous observations under high-frequency asymptotics. Our approach…

Statistics Theory · Mathematics 2014-07-02 Markus Bibinger , Nikolaus Hautsch , Peter Malec , Markus Reiß

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…

Biological Physics · Physics 2020-08-10 Robert Marsland , Wenping Cui , Jordan M. Horowitz

Being able to measure time, whether directly or indirectly, is a significant advantage for an organism. It permits it to predict regular events, and prepare for them on time. Thus, clocks are ubiquitous in biology. In the present paper, we…

Other Quantitative Biology · Quantitative Biology 2017-06-23 Andrei D. Robu , Christoph Salge , Chrystopher L. Nehaniv , Daniel Polani

For atomic frequency standards in which fluctuations of the local oscillator (LO) frequency are the dominant noise source, we examine the role of the servo algorithm that predicts and corrects these frequency fluctuations. We derive the…

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…

Mathematical Physics · Physics 2016-03-03 Martin Fraas

In this paper, an alternative approximation to the innovation method is introduced for the parameter estimation of diffusion processes from partial and noisy observations. This is based on a convergent approximation to the first two…

Optimization and Control · Mathematics 2013-12-19 J. C. Jimenez

Circadian rhythms are biological rhythms of approximately 24 h that persist even under constant conditions without environmental daily cues. The molecular circadian clock machinery generates the physiological rhythms, which can be…

Molecular Networks · Quantitative Biology 2022-10-05 Hotaka Kaji , Fumito Mori , Hiroshi Ito

Accurate estimation of the human circadian phase plays an important role in personalized health monitoring, but most existing wearable-based approaches operate retrospectively and require full circadian cycle recordings, leading to high…

Signal Processing · Electrical Eng. & Systems 2026-05-05 Mengzhu Xu , Nemanja Cabrilo , Merel van Gilst , Jean-Paul Linnartz

Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but also allows fluctuation measurements which may reveal the structure and dynamics of the underlying biochemical network.…

Biological Physics · Physics 2018-04-11 Harmen Wierenga , Pieter Rein ten Wolde , Nils B. Becker

In trapped-atom clocks, the primary source of decoherence is often the phase noise of the oscillator. For this case, we derive theoretical performance gains by combining several atomic ensembles. For example, M ensembles of N atoms can be…

Quantum Physics · Physics 2013-11-15 T. Rosenband , D. R. Leibrandt

We consider the task of estimating the randomly fluctuating phase of a continuous-wave beam of light. Using the theory of quantum parameter estimation, we show that this can be done more accurately when feedback is used (adaptive phase…

Quantum Physics · Physics 2009-11-10 D. T. Pope , H. M. Wiseman , N. K. Langford

Hyper-Ramsey protocols effectively reduce AC-Stark shifts in probing ultra-narrow optical clock transitions but they remain sensitive to laser intensity noise, decoherence, frequency drifts, and low-frequency perturbations. We address these…

Atomic Physics · Physics 2025-12-25 T. Zanon-Willette , B. Ilikj , D. Wilkowski , B. Darquié , N. V. Vitanov
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