Related papers: Are physiological oscillations 'physiological'?
Many intracellular processes continue to oscillate during the cell cycle. Although it is not well-understood how they are affected by discontinuities in the cellular environment, the general assumption is that oscillations remain robust…
Circadian rhythms are archetypical examples of nonlinear oscillations. While these oscillations are usually attributed to circuits of biochemical interactions among clock genes and proteins, recent experimental studies reveal that they are…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
Embedding efficient command operation into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reactions that act as units of computation. The answer is to design…
Oscillatory chemical reactions are functional components in a variety of biological contexts. In chemistry, the construction and identification of even rudimentary oscillators remain elusive and lack a general framework. Using…
In recent years it is increasingly being recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that…
We study chemical oscillators in the presence of phase separation. By imposing timescale separation between slow reactions and fast diffusion, we define a dynamics at phase equilibrium for the relevant degrees of freedom. We demonstrate…
Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian…
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…
Feedback loops are major components of biochemical systems. Many systems show multiple such (positive or negative) feedback loops. Nevertheless, very few quantitative analyses address the question how such multiple feedback loops evolved.…
Brain rhythms seem central to understanding the neurophysiological basis of human cognition. Yet, despite significant advances, key questions remain unresolved. In this comprehensive position paper, we review the current state of the art on…
Self-oscillations underlie many natural phenomena such as heartbeat, ocean waves, and the pulsation of variable stars. From pendulum clocks to the behavior of animal groups, self-oscillation is one of the keys to the understanding of…
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 dynamics of one species chemical kinetics is studied. Chemical reactions are modelled by means of continuous time Markov processes whose probability distribution obeys a suitable master equation. A large deviation theory is formally…
A wide range of organisms use circadian clocks to keep internal sense of daily time and regulate their behavior accordingly. Most of these clocks use intracellular genetic networks based on positive and negative regulatory elements. The…
Yeast glycolysis is considered the prototype of dissipative biochemical oscillators. In cellular conditions, under sinusoidal source of glucose, the activity of glycolytic enzymes can display either periodic, quasiperiodic or chaotic…
Motile cilia are a striking example of functional cellular organelle, conserved across all the eukaryotic species. Motile cilia allow swimming of cells and small organisms and transport of liquids across epithelial tissues. Whilst the…
Although osmosis is a familiar phenomenon, and of pivotal importance in natural systems, it is seldom explained how it might work on the molecular level (if treated at all in physics text books). The standard treatment of osmosis in…
Pancreatic islets, controlling glucose homeostasis, consist of \alpha, \beta, and \delta\ cells. It has been observed that \alpha\ and \beta\ cells generate out-of-phase synchronization in the release of glucagon and insulin,…
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…