Related papers: Distinguishing Feedback Mechanisms in Clock Models
Intrinsically disordered protein regions (IDRs) are found across all domains of life and are characterized by a lack of stable 3D structure. Nevertheless, IDRs play critical roles in the most tightly regulated cellular processes, including…
Physiological networks are usually made of a large number of biological oscillators evolving on a multitude of different timescales. Phase oscillators are particularly useful in the modelling of the synchronization dynamics of such systems.…
Using computer simulations, we study the dynamics of colloidal particles with time-delayed feedback interactions. In particular, here we consider "feedback-pullers", i.e.~colloidal particles that are pulled away from their current position…
Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules…
Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling…
Common models of synchronizable oscillatory systems consist of a collection of coupled oscillators governed by a collection of differential equations. The ubiquitous Kuramoto models rely on an {\em a priori} fixed connectivity pattern…
Coupled electronic oscillators have recently been explored as a compact, integrated circuit- and room temperature operation- compatible hardware platform to design Ising machines. However, such implementations presently require the…
Carpets of actively bending cilia represent arrays of biological oscillators that can exhibit self-organized metachronal synchronization in the form of traveling waves of cilia phase. This metachronal coordination supposedly enhances fluid…
According to the chemical reaction network theory, the topology of a certain class of chemical reaction networks, regardless of the kinetic details, sets a limit on the dynamical properties that a particular network can potentially admit;…
The circadian rhythm plays a crucial role in regulating biological processes, and its disruption is linked to various health issues. Identifying small molecules that influence the circadian period is essential for developing targeted…
We develop a detailed theoretical framework for various types of transcription factor gene oscillators. We further demonstrate that one can build genetic-oscillators which are tunable and robust against perturbations in the critical control…
We consider the decision making by mammalian cells, looking them as dynamic systems with rhythms. We calculate the effective dimension of the cell division model of the healthy mammalian cells consistent with the data: it is described via a…
Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression have recently been studied intensively…
Calcium and reactive oxygen species (ROS) interact with each other and play an important role in cell signaling networks. Based on the existing mathematical models, we develop an age-dependent feedback control model to simulate the…
We study the dynamics of a circadian oscillator model which was proposed by Tyson, Hong, Thron and Novak. This model indicates a molecular mechanism for the circadian rhythm in Drosophila. After giving a detailed study of the equilibria, we…
Many intracellular processes continue to oscillate during the cell cycle. Although it is not well-understood how they are affected by discontinuities in the cellular environment, the general assumption is that oscillations remain robust…
Weakly coupled limit cycle oscillators can be reduced into a system of weakly coupled phase models. These phase models are helpful to analyze the synchronization phenomena. For example, a phase model of two oscillators has a one-dimensional…
In this work a classical linear harmonic oscillator, evolving during a small time interval (so that simple non-linear, second order Taylor approximation of the dynamics is satisfied) and restarting (by a mechanism) in a strictly chosen…
Autonomous oscillators, such as clocks and lasers, produce periodic signals \emph{without} any external frequency reference. In order to sustain stable periodic motions, there needs to be external energy supply as well as nonlinearity built…
Oscillatory behavior is ubiquitous in many natural and engineered systems, often emerging through self-regulating mechanisms. In this paper, we address the challenge of stabilizing a desired oscillatory pattern in a networked system where…