Related papers: Distinguishing Feedback Mechanisms in Clock Models
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 urea-urease clock reaction is a pH switch from acid to basic that can turn into a pH oscillator if it occurs inside a suitable open reactor. We study the confinement of the reaction to lipid vesicles, which permit the exchange with an…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
Biochemical oscillations are prevalent in living organisms. Systems with a small number of constituents cannot sustain coherent oscillations for an indefinite time because of fluctuations in the period of oscillation. We show that the…
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…
The in vivo circadian clock in single cyanobacteria is studied here by time-lapse fluorescence microscopy when the temperature is lowered below 25{\deg}C . We first disentangle the circadian clock behavior from the bacterial cold shock…
Circadian oscillation provides selection advantages through synchronization to the daylight cycle. However, a reliable clock must be designed through two conflicting properties: entrainability to synchronize internal time with periodic…
Feedback alignment and related weight-transport-free algorithms are often proposed as biologically plausible alternatives to backpropagation, yet they are typically formulated in discrete phases with implicitly synchronized forward and…
Multiple organs in a living system respond to environmental changes, and the signals from the organs regulate the physiological environment. Inspired by this biological feedback, we propose a simple autonomous system of active rotators to…
Engineering genetic networks to be both predictable and robust is a key challenge in synthetic biology. Synthetic circuits must reliably function in dynamic, stochastic and heterogeneous environments, and simple circuits can be studied to…
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…
Oscillations in nonequilibrium noisy systems are important physical phenomena. These oscillations can happen in autonomous biochemical oscillators such as circadian clocks. They can also manifest as subharmonic oscillations in periodically…
Feedback delay has been identified as a key ingredient in the quorum sensing synchronization of synthetic gene oscillators. While this influence has been evidenced at the theoretical level in a simplified system of degrade-and-fire…
Circadian rhythms are acquired through evolution to increase the chances for survival through synchronizing with the daylight cycle. Reliable synchronization is realized through two trade-off properties: regularity to keep time precisely,…
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…
Proper vertebrae formation relies on a tissue-wide oscillator called the segmentation clock. Individual cellular oscillators in the presomitic mesoderm are modulated by intercellular coupling and external signals, leading to the propagation…
Ring oscillators are biochemical circuits consisting of a ring of interactions capable of sustained oscillations. The non-linear interactions between genes hinder the analytical insight into their function, usually requiring computational…
Embedding efficient calculation instructions into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reaction modules that act as units of computation and make…
Periodic patterns in dynamical behaviours of biological models described by simple form differential delay equations are studied. Mathematical models are given by a class of scalar delay differential equations with a multiplicative time…
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…