Related papers: Distinguishing Feedback Mechanisms in Clock Models
We study the effects of time delayed linear and nonlinear feedbacks on the dynamics of a single Hopf bifurcation oscillator. Our numerical and analytic investigations reveal a host of complex temporal phenomena such as phase slips,…
The green microscopic alga Ostreococcus tauri has recently emerged as a promising model for understanding how circadian clocks, which drive the daily biological rythms of many organisms, synchronize to the day/night cycle in changing…
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…
We have studied theoretically the basic operation of a quantum feedback loop designed to maintain the desired phase of quantum coherent oscillations in a two-level system. Such feedback can suppress the dephasing of oscillations due to…
Bioreactors are widely used in many industries to generate a range of products using various host cells e.g., yeast, insect, and mammalian cells. Depending on the process, product, and host cell, some bioreactors exhibit sustained periodic…
Collective oscillation of cells in a population has been reported under diverse biological contexts and with vastly different molecular constructs. Could there be common principles similar to those that govern spontaneous oscillation in…
Living systems regulate many aspects of their behavior through periodic oscillations of molecular concentrations, which function as `biochemical clocks.' These clocks are intrinsically subject to thermal fluctuations, so that the duration…
We analyze the nature and performance of clocks formed by stabilizing an oscillator to the phase difference between two paths of an atom interferometer. The phase evolution has been modeled as being driven by the proper-time difference…
The center of mass motion of trapped ions and neutral atoms is suitable for approximation by a time-dependent driven quantum harmonic oscillator whose frequency and driving strength may be controlled with high precision. We show the time…
Circadian clocks exhibit the robustness of period and plasticity of phase against environmental changes such as temperature and nutrient conditions. Thus far, however, it is unclear how both are simultaneously achieved. By investigating…
We have studied theoretically the basic operation of a quantum feedback loop designed to maintain a desired phase of quantum coherent oscillations in a single solid-state qubit. The degree of oscillations synchronization with external…
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 paper highlights the role of a positive feedback gating mechanism at the cellular level in the robust- ness and modulation properties of rhythmic activities at the circuit level. The results are presented in the context of half-center…
Self-sustained oscillators (SSOs) is a commonly used method to generate classical clock signals and SSOs using delayed feedback have been developed commercially which possess ultra-low phase noise and drift. Research into the development of…
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…
Automated verification of living organism models allows us to gain previously unknown knowledge about underlying biological processes. In this paper, we show the benefits to use parametric time Petri nets in order to analyze precisely the…
Entrainment experiments on the vertebrate segmentation clock have revealed that embryonic oscillators actively change their internal frequency to adapt to the driving signal. This is neither consistent with a one-dimensional clock model nor…
In this paper, we study the stability of an Ordinary Differential Equation (ODE) usually referred to as Cyclic Feedback Loop, which typically models a biological network of molecules where each molecule regulates its successor in a cycle.…
Simple form scalar differential equation with delay and non-linear negative periodic feedback is considered. The existence of slowly oscillating periodic solutions with the same period as the feedback coefficient is shown numerically within…
We study the impact of light on the mammalian circadian system using the theory of phase response curves. Using a recently developed ansatz we derive a low-dimensional macroscopic model for the core circadian clock in mammals.…