Related papers: Distinguishing Feedback Mechanisms in Clock Models
We present an analytical solution of the single photon quantum feedback in a cavity quantum electrodynamics system based on a half cavity set-up coupled to a structured continuum. The exact analytical expression we obtain allows us to…
A model of Drosophila circadian rhythm generation was developed to represent feedback loops based on transcriptional regulation of per, Clk (dclock), Pdp-1, and vri (vrille). The model postulates that histone acetylation kinetics make…
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…
Statistical estimation theory determines the optimal way of estimating parameters of a fluctuating noisy signal. However, if the estimation is performed on unreliable hardware, a sub-optimal estimation procedure can outperform the…
We consider application of the multiple time delayed feedback for control of anharmonic (nonlinear) oscillators subject to noise. In contrast to the case of a single delay feedback, the multiple one exhibits resonances between feedback and…
Rhythms in electrical activity in the membrane of cells in the suprachiasmatic nucleus (SCN) are crucial for the function of the circadian timing system, which is characterized by the expression of the so-called clock genes. Intracellular…
Cellular appendages conferring motility, such as flagella or cilia, are known to synchronise their periodic beats. The origin of synchronisation is a combination of long-range hydrodynamic interactions with physical mechanisms allowing the…
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell-types. This developmental differentiation process typically involves intracellular regulatory and stochastic…
In classical physics, clocks are open dissipative systems driven from thermal equilibrium and necessarily subject to thermal noise. We describe a quantum clock driven by entropy reduction through measurement. The mechanism consists of a…
By the example of a kicked quartic oscillator we investigate the dynamics of classically chaotic quantum systems with few degrees of freedom affected by persistent external noise. Stability and reversibility of the motion are analyzed in…
The ability of a circadian system to entrain to the 24-hour light-dark cycle is one of its most important properties. A new tool, called the entrainment map, was recently introduced to study this process for a single oscillator. Here we…
After introducing commutativity concept and summarizing the relevant literature, this work is focused on the commutativity of feedback conjugates. It is already known that a linear time-varying differential system describing a single…
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…
For noisy self-sustained oscillators, both reliability, stability of a response to a noisy driving, and coherence understood in the sense of constancy of oscillation frequency belong to the main characteristics. Though the both…
We use the oscillating Min proteins of Escherichia coli as a prototype system to illustrate the current state and potential of modeling protein dynamics in space and time. We demonstrate how a theoretical approach has led to striking new…
The production process of integrated electronic circuitry inherently leads to large heterogeneities on the component level. For electronic clock networks this implies detuned intrinsic frequencies and differences in coupling strength and…
We present a derivation of the structure and dynamics of a ticking clock by showing that for finite systems a single natural principle serves to distinguish what we understand as ticking clocks from time-keeping systems in general. As a…
To gain insight into the nature of biological synchronization at the microscopic scale, we here investigate the hydrodynamic synchronization between conically rotating objects termed nodal cilia. A mechanical model of three rotating cilia…
Our study is motivated by the prospect of several metastable states in the Sb$ ^{+} $, Au$ ^{+} $, and Hg$ ^{2+} $ ions being used as possible candidates for optical clocks. We calculate several atomic properties relevant to the development…
In this Supporting Information, we provide background information on our model of the in vitro Kai system and the calculations that we have performed. We will closely follow the outline of the main text.