Related papers: Protein sequestration versus Hill-type repression …
We present a general relativistic model of a spherical shell of matter with a perfect fluid on its surface coupled to an internal oscillator, which generalizes a model recently introduced by the authors to construct a self-gravitating…
The KaiABC circadian clock from cyanobacteria is the only known three-protein oscillatory system which can be reconstituted outside the cell and which displays sustained periodic dynamics in various molecular state variables. Despite many…
Oscillations represent a ubiquitous phenomenon in biological systems. The conventional models of biological periodic oscillations are usually proposed as interconnecting transcriptional feedback loops. Some specific proteins function as…
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…
The circadian clock can adapt itself to external cues, but the molecular mechanisms and regulatory networks governing circadian oscillations' transient adjustments are still largely unknown. Here we consider the specific case of circadian…
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…
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 suprachiasmatic nucleus (SCN), also known as the circadian master clock, consists of a large population of oscillator neurons. Together, these neurons produce a coherent signal that drives the body's circadian rhythms. What properties…
From a coarse-grained perspective the motif of a self-activating species, activating a second species which acts as its own repressor, is widely found in biological systems, in particular in genetic systems with inherent oscillatory…
In the mammalian suprachiasmatic nucleus (SCN), a population of noisy cell-autonomous oscillators synchronizes to generate robust circadian rhythms at the organism-level. Within these cells two isoforms of Cryptochrome, Cry1 and Cry2,…
To function as gene regulatory elements in response to environmental signals, riboswitches must adopt specific secondary structures on appropriate time scales. We employ kinetic Monte Carlo simulation to model the time-dependent folding…
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…
The dynamics of an unique type of clock mechanism known as grasshopper escapement is investigated with the aim of evaluating its accuracy in a noisy environment. It is demonstrated that the clock's precision scales linearly with the rate of…
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
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…
Atomic clocks are crucial for science and technology, but their sensitivity is often restricted by the standard quantum limit. To surpass this limit, correlations between particles or interrogation times must be leveraged. Although the…
Entrainment experiments on the vertebrate segmentation clock have revealed that embryonic oscillators actively change their internal frequency to adapt to the driving signal. This is neither consistent with a one-dimensional clock model nor…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…