Related papers: Biological Circuits: Analysis of a Biological Osci…
Circadian rhythms are endogenous 24-hour oscillations that regulate physiology, metabolism, sleep-wake cycles, and cellular homeostasis. Drosophila melanogaster, a genetically tractable model organism, has played a foundational role in…
Biochemical oscillations are ubiquitous in living organisms. In an autonomous system, not influenced by an external signal, they can only occur out of equilibrium. We show that they emerge through a generic nonequilibrium phase transition,…
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…
This work explores the dynamic properties of test particles surrounding a distorted, deformed compact object. The astrophysical motivation was to choose such background, which could constitute a more reasonable model of a real situation…
Experiments that compare rhythmic properties across different genetic alterations and entrainment conditions underlie some of the most important breakthroughs in circadian biology. A robust estimation of the rhythmic properties of the…
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.
We consider a radiation from a uniformly accelerating harmonic oscillator whose minimal coupling to the scalar field changes suddenly. The exact time evolutions of the quantum operators are given in terms of a classical solution of a forced…
Drosophila's circadian clock can be perturbed by magnetic fields, as well as by lithium administration. Cryptochromes are critical for the circadian clock. Further, the radical pairs in cryptochrome also can explain magnetoreception in…
Almost all organisms show some kind of time periodicity in their behavior. Especially in mammals the neurons of the suprachiasmatic nucleus form a biological clock regulating the activity-inactivity cycle of the animal. This clock is…
In genomic applications, there is often interest in identifying genes whose time-course expression trajectories exhibit periodic oscillations with a period of approximately 24 hours. Such genes are usually referred to as circadian, and…
A harmonic oscillator with time-dependent mass $m(t)$ and a time-dependent (squared) frequency $\omega^2(t)$ occurs in the modelling of several physical systems. It is generally believed that systems, with $m(t)>0$ and $\omega^2(t)>0$…
Genetically encoded regulatory circuits control biological function. A major focus of systems biology is to understand these circuits by establishing the relationship between specific structures and functions. Of special interest are…
We describe the use of quasiperiodic oscillators for computation and control of robots. We also describe their relationship to central pattern generators in simple organisms and develop a group theory for describing the dynamics of these…
Protein sequestration motifs appear in many biological regulatory networks and introduce special properties into the network dynamics. Sequestration can be described as a mode of inactivation of a given protein by its binding to a second…
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 quantum quartic oscillator is investigated in order to test the many-body technique of the continuous unitary transformations. The quartic oscillator is sufficiently simple to allow a detailed study and comparison of various…
Oscillatory gene circuits are ubiquitous to biology and are involved in fundamental processes of cell cycle, circadian rhythms and developmental systems. The synthesis of small, non-natural oscillatory genetic circuits have been…
Oscillations lie at the core of many biological processes, from the cell cycle, to circadian oscillations and developmental processes. Time-keeping mechanisms are essential to enable organisms to adapt to varying conditions in environmental…
Biological rhythms are generated by pacemaker organs, such as the heart pacemaker organ (the sinoatrial node) and the master clock of the circadian rhythms (the suprachiasmatic nucleus), which are composed of a network of autonomously…
It is shown that periodic orbits can occur in Cholette's bioreactor model working under the influence of a PI-controller. We find a diffeomorphic coordinate transformation that turns this controlled enzymatic reaction system into a…