Related papers: Promoter methylation in a mixed feedback loop circ…

Noise can induce coherent oscillations in excitable systems without periodic orbits. Here, we establish a method to derive a hybrid system approximating the noise-induced coherent oscillations in excitable systems and further perform phase…

Positive feedback and cooperativity in the regulation of gene expression are generally considered to be necessary for obtaining bistable expression states. Recently, a novel mechanism of bistability termed emergent bistability has been…

Cancer development is associated with aberrant DNA methylation, including increased stochastic variability. Statistical tests for discovering cancer methylation biomarkers have focused on changes in mean methylation. To improve the power of…

We formulate a mathematical model for daily activities of a cow (eating, lying down, and standing) in terms of a piecewise affine dynamical system. We analyze the properties of this bovine dynamical system representing the single animal and…

We propose a revisited version of the in vivo model of the cyanobacterial circadian clock. Our aim is to address the lack of robustness predicted for the mutant cyanobacteria without transcriptional regulation of the original model. For…

Generative probabilistic models have shown promise in designing artificial RNA and protein sequences but often suffer from high rates of false positives, where sequences predicted as functional fail experimental validation. To address this…

Goodwin's model is a cornerstone in the study of dynamical systems within macroeconomics, explaining the interaction between employment ratio and wage share in a closed economy. Analogous to predator-prey dynamics in mathematical economics,…

We study the periodic forced response of a system of two limit cycle oscillators that interact with each other via a time delayed coupling. Detailed bifurcation diagrams in the parameter space of the forcing amplitude and forcing frequency…

The stochastic FitzHugh-Nagumo model with time delayed-feedback is often studied in excitable regime to demonstrate the time-delayed control of coherence resonance. Here, we show that the impact of time-delayed feedback in the…

Widespread deployment of societal-scale machine learning systems necessitates a thorough understanding of the resulting long-term effects these systems have on their environment, including loss of trustworthiness, bias amplification, and…

Genetic oscillators play important roles in cell life regulation. The regulatory efficiency usually depends strongly on the emergence of stable collective dynamic modes, which requires designing the interactions between genetic networks. We…

Entrainment of randomly coupled oscillator networks by periodic external forcing applied to a subset of elements is numerically and analytically investigated. For a large class of interaction functions, we find that the entrainment window…

The century-long Michaelis-Menten rate law and its modifications in the modeling of biochemical rate processes stand on the assumption that the concentration of the complex of interacting molecules, at each moment, rapidly approaches an…

The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…

Oscillations play a major role in a number of biological systems, from predator-prey models of ecology to circadian clocks. In this paper we focus on the question of whether oscillations exist within dual-site phosphorylation systems.…

I show that incoherent dynamics can lead to metrological advantages in quantum sensing. The results rely on the fact that incoherent dynamics lead to an additive contribution to the quantum Fisher information about time. Such an additive…

Synchronization is a widespread phenomenon observed in physical, biological, and social networks, which persists even under the influence of strong noise. Previous research on oscillators subject to common noise has shown that noise can…

Interrogating the evolution of biological changes at early stages of life requires longitudinal profiling of molecules, such as DNA methylation, which can be challenging with children. We introduce a probabilistic and longitudinal machine…

A van der Pol self sustained oscillator with higher order nonlinearity exhibits a rich dynamics, with multiple periodic attractors, and still the model allows analytical approximations. Some of these properties can be conveniently exploited…

DNA cytosine methylation is a critical epigenetic mark regulating gene expression and thus playing an important role in development and differentiation across eukaryotes. Existing tools for high-throughput methylation analysis often lack…