Related papers: Biological rhythms generated by a single activator…
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 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…
Biochemical oscillations are ubiquitous in nature and allow organisms to properly time their biological functions. In this paper, we consider minimal Markov state models of nonequilibrium biochemical networks that support oscillations. We…
Reaction-diffusion (RD) mechanisms in chemical and biological systems can yield a variety of patterns that may be functionally important. We show that diffusive coupling through the inactivating component in a generic model of coupled…
Embedding sequential computations in biochemical environments is challenging because the computations are carried out by chemical reactions, which are inherently disordered. In this paper we apply modular design to specific calculations…
Originating from the pioneering study of Alan Turing, the bifurcation analysis predicting spatial pattern formation from a spatially uniform state for diffusing morphogens or chemical species that interact through nonlinear reactions is a…
Circadian (~24hr) clocks are self-sustained endogenous oscillators with which organisms keep track of daily and seasonal time. Circadian clocks frequently rely on interlocked transcriptional- translational feedback loops to generate rhythms…
The circadian clocks keeping time of day in many living organisms rely on self-sustained biochemical oscillations which can be entrained by external cues, such as light, to the 24-hour cycle induced by Earth rotation. However, environmental…
Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory…
Reaction-diffusion systems can describe a wide class of rhythmic spatiotemporal patterns observed in chemical and biological systems, such as circulating pulses on a ring, oscillating spots, target waves, and rotating spirals. These…
Nearly all circadian clocks maintain a period that is insensitive to temperature changes, a phenomenon known as temperature compensation (TC). Yet, it is unclear whether there is any common feature among different systems that exhibit TC.…
The mammalian circadian system comprises a network of cell-autonomous oscillators, spanning from the central clock in the brain to peripheral clocks in other organs. These clocks are tightly coordinated to orchestrate rhythmic physiological…
Negative and positive transcriptional feedback loops are present in natural and synthetic genetic oscillators. A single gene with negative transcriptional feedback needs a time delay and sufficiently strong nonlinearity in the transmission…
We prove that the famous diffusive Brusselator model can support more complicated spatial-temporal wave structure than the usual temporal-oscillation from a standard Hopf bifurcation. In our investigation, we discover that the diffusion…
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…
Reaction equations of homogeneously mixed pollutants in the atmosphere can lead to non-stationary periodic solutions. It is important to know in which respect these solutions are modified under the influence of the atmospheric currents. We…
We describe a mechanism for pronounced biochemical oscillations, relevant to microscopic systems, such as the intracellular environment. This mechanism operates for reaction schemes which, when modeled using deterministic rate equations,…
The universal equations describing collective oscillations of the multidomain patterns of small period in an arbitrary $d$-dimensional reaction-diffusion system of the activator-inhibitor type are asymptotically derived. It is shown that…
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…
It is possible that there are post-translational circadian oscillators that continue functioning in the absence of negative feedback transcriptional repression in many cell types from diverse organisms. Apart from the KaiABC system from…