Related papers: Biological rhythms generated by a single activator…
Circadian rhythms are biological rhythms of approximately 24 h that persist even under constant conditions without environmental daily cues. The molecular circadian clock machinery generates the physiological rhythms, which can be…
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…
The circadian clock is the molecular mechanism responsible for the adaptation to daily rhythms in living organisms. Oscillations and fluctuations in environmental conditions regulate the circadian clock through signaling pathways. We study…
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…
Organisms often use cyclic changes in the concentrations of chemicals species to precisely time biological functions. Underlying these biochemical clocks are chemical reactions and transport processes, which are inherently stochastic.…
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…
In coupled reaction-diffusion systems, modes with two different length scales can interact to produce a wide variety of spatiotemporal patterns. Three-wave interactions between these modes can explain the occurrence of spatially complex…
Biochemical circadian rhythm oscillations play an important role in many signalling mechanisms. In this work, we explore some of the biophysical mechanisms responsible for sustaining robust oscillations by constructing a minimal but…
Spontaneous rhythmic oscillations are widely observed in various real-world systems. In particular, biological rhythms, which typically arise via synchronization of many self-oscillatory cells, often play important functional roles in…
The collective dynamics seen in a wide variety of chemical, biological and ecological systems involve interactions between relaxation oscillators that typically involve fast activation process coupled with a slower inactivation. In this…
Circadian rhythms in living organisms are temporal orders emerging from biochemical circuits driven out of equilibrium. Here, considering the KaiABC system, a minimal model in the synthetic biology, we study how the oscillation emerges from…
We study a reaction diffusion system of the activator-inhibitor type with inhomogeneous reaction terms showing spatiotemporal chaos. We analyze the topological properties of the unstable periodic orbits in the slow chaotic dynamics…
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…
Protein sequestration motifs appear in many biological regulatory networks and introduce special properties into the network dynamics. Sequestration can be described as a mode of inactivation of a given protein by its binding to a second…
Turing's mechanism is often invoked to explain periodic patterns in nature, although direct experimental support is scarce. Turing patterns form in reaction-diffusion systems when the activating species diffuse much slower than the…
The spontaneous generation of electrical activity underpins a number of essential physiological processes, and is observed even in tissues where specialized pacemaker cells have not been identified. The emergence of periodic oscillations in…
Chemically fueled supramolecular systems can exhibit complex, time-dependent behaviors reminiscent of living matter when maintained far from equilibrium by continuous energy or fuel consumption. Here, we introduce a minimal…
Oscillatory chemical reactions often serve as a timing clock of cellular processes in living cells. The temporal dynamics of protein concentration levels is thus of great interest in biology. Here we propose a theoretical framework to…
Transport in a one-dimensional symmetric device can be activated by the combination of thermal noise and a bi-harmonic drive. For the study case of an overdamped Brownian particle diffusing on a periodic one-dimensional substrate, we…
Many physical, chemical and biological processes rely on intrinsic oscillations to employ resonance responses to external stimuli of certain frequency. Such resonance phenomena in biological systems are typically explained by one of two…