Related papers: Modeling Transient Changes in Circadian Rhythms
Oscillation is an important cellular process that regulates timing of different vital life cycles. However, in the noisy cellular environment, oscillations can be highly inaccurate due to phase fluctuations. It remains poorly understood how…
The Jansen-Rit model of a cortical column in the cerebral cortex is widely used to simulate spontaneous brain activity (EEG) and event-related potentials. It couples a pyramidal cell population with two interneuron populations, of which one…
Cells use genetic switches to shift between alternate gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Here, we study the dynamics of switching in a generic-feedback on/off switch. Unlike…
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…
Theoretical and experimental studies have shown that the fluctuations of in vivo systems break the fluctuation-dissipation theorem. One can thus ask what information is contained in the correlation functions of protein concentrations and…
This work is motivated by a desire to understand transitions between stable equilibria observed in Stommel's 1961 thermohaline circulation model. We adapt the model, including a forcing parameter as a dynamic slow variable. The resulting…
We consider a periodic quantum clock based on cooperative resonance fluorescence at zero temperature. In the quantum case, this system has an exact steady state and the limit cycle appears in conditional quantum dynamics under homodyne…
Heat fluctuations of a harmonic oscillator in contact with a thermostat and driven out of equilibrium by an external deterministic force are studied experimentally and theoretically within the context of Fluctuation Theorems. We consider…
Detecting early warning signals in climatic time series is essential for anticipating critical transitions and tipping points. Common statistical indicators include increased variance and lag-one autocorrelation prior to bifurcation points.…
Chemical reaction rates must increasingly be determined in systems that evolve under the control of external stimuli. In these systems, when a reactant population is induced to cross an energy barrier through forcing from a temporally…
Cellular responses to death-promoting stimuli typically proceed through a differentiated multistage process, involving a lag phase, extensive death, and potential adaptation. Deregulation of this chain of events is at the root of many…
A number of brown dwarfs are now known to be variable with observed amplitudes as large as 10-30% at some wavelengths. While spatial inhomogeneities in cloud coverage and thickness are likely responsible for much of the observed…
Fluctuations and noise may alter the behavior of dynamical systems considerably. For example, oscillations may be sustained by demographic fluctuations in biological systems where a stable fixed point is found in the absence of noise. We…
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…
Circadian clocks must be able to entrain to time-varying signals to keep their oscillations in phase with the day-night rhythm. On the other hand, they must also exhibit input compensation: their period must remain about one day in…
This paper augments the existing macroscopic circuit noise model for phase noise in relaxation oscillators by showing the microscopic origins of the noise and explains temperature dependency. The noise arises from fluctuation of the energy…
A new approach to investigate noise spikes due to regeneration in a relaxation oscillator is proposed. Noise spikes have not been satisfactorily accounted for in traditional phase noise models. This paper attempts to explain noise…
To estimate the time, many organisms, ranging from cyanobacteria to animals, employ a circadian clock which is based on a limit-cycle oscillator that can tick autonomously with a nearly 24h period. Yet, a limit-cycle oscillator is not…
Deep, overparameterized regression models are notorious for their tendency to overfit. This problem is exacerbated in heteroskedastic models, which predict both mean and residual noise for each data point. At one extreme, these models fit…
We simulate the electrical properties of a device realized by a G protein coupled receptor (GPCR), embedded in its membrane and in contact with two metallic electrodes through which an external voltage is applied. To this purpose, recently,…