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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…
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.…
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…
On the microscopic level, biological signal transmission relies on coordinated structural changes in allosteric proteins that involve sensor and effector modules. The timescales and microscopic details of signal transmission in proteins are…
Discrete time crystals are periodically driven systems that display spontaneous symmetry breaking of time translation invariance in the form of indefinite subharmonic oscillations. We introduce a thermodynamically consistent model for a…
There are many natural, physical, and biological systems that exhibit multiple time scales. For example, the dynamics of a population of ticks can be described in continuous time during their individual life cycle yet discrete time is used…
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…
This paper analyzes, in the context of a prokaryotic cell, the stochastic variability of the number of proteins when there is a control of gene expression by an autoregulation scheme. The goal of this work is to estimate the efficiency of…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…
Observations that rates of molecular evolution vary widely within and among lineages have cast doubts upon the existence of a single molecular clock. Differences in the timing of evolutionary events estimated from genetic and fossil…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
The green microscopic alga Ostreococcus tauri has recently emerged as a promising model for understanding how circadian clocks, which drive the daily biological rythms of many organisms, synchronize to the day/night cycle in changing…
Stochastic clocks represent a class of time change methods for incorporating trading activity into continuous-time financial models, with the ability to deal with typical asymmetrical and tail risks in financial returns. In this paper we…
The oscillatory dynamics of natural and man-made systems can be disrupted by their time-varying interactions, leading to oscillation quenching phenomena in which the oscillations are suppressed. We introduce a framework for analyzing,…
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…
Temporal resolution of visual information processing is thought to be an important factor in predator-prey interactions, shaped in the course of evolution by animals' ecology. Here I show that light can be considered to have a dual role of…
We study a system of dynamical units, each of which shows excitable or oscillatory behavior, depending on the choice of parameters. When we couple these units with repressive bonds, we can control the duration of collective oscillations for…
The study of synchronization in biological systems is essential for the understanding of the rhythmic phenomena of living organisms at both molecular and cellular levels. In this paper, by using simple dynamical systems theory, we present a…
Using the model of a generalized Van der Pol oscillator in the regime of subcritical Hopf bifurcation we investigate the influence of time delay on noise-induced oscillations. It is shown that for appropriate choices of time delay either…
The temporal behaviour of segmentation clock oscillations show phase synchrony via mean field like coupling of delta protein restricting to nearest neighbours only, in a configuration of cells arranged in a regular three dimensional array.…