Related papers: Promoter methylation in a mixed feedback loop circ…
To understand the sophisticated control mechanisms of the human's endocrine system is a challenging task that is a crucial step towards precise medical treatment of many disfunctions and diseases. Although mathematical models describing the…
The synthetic construction of intracellular circuits is frequently hindered by a poor knowledge of appropriate kinetics and precise rate parameters. Here, we use generalized modeling (GM) to study the dynamical behavior of topological…
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,…
We present a model of discrete quantum evolution based on quantum correlations between the evolving system and a reference quantum clock system. A quantum circuit for the model is provided, which in the case of a constant Hamiltonian is…
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.…
Using the model of a FitzHugh-Nagumo system in the excitable regime we investigate the influence of time-delayed feedback on noise-induced chimera states in a network with nonlocal coupling, i.e., coherence resonance chimeras. It is shown…
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 show the existence of a high interrelation between the different loops that may appear in a DNA segment. Conformational changes in a chain segment caused by the formation of a particular loop may either promote or prevent the appearance…
The phenomenon of delay-induced resonance implies that in a nonlinear system a time-delay term may be used as an effective enhancer of the oscillations caused by an external forcing maintaining the same frequency. This is possible for the…
The gene networks that comprise the circadian clock modulate biological function across a range of scales, from gene expression to performance and adaptive behaviour. The clock functions by generating endogenous rhythms that can be…
We review the construction and evolution of mathematical models of the Arabidopsis circadian clock, structuring the discussion into two distinct historical phases of modeling strategies: extension and reduction. The extension phase explores…
It is possible that there are post-translational circadian oscillators that continue functioning in the absence of negative feedback transcriptional repression in many cell types from diverse organisms. Apart from the KaiABC system from…
Autonomous circadian clocks drive daily rhythms in physiology and behaviour. A network of coupled neurons, the suprachiasmatic nucleus (SCN), serves as a robust self-sustained circadian pacemaker. Synchronization of this timer to the…
The conformational kinetics of enzymes can be reliably revealed when they are governed by Markovian dynamics. Hidden Markov Models (HMMs) are appropriate especially in the case of conformational states that are hardly distinguishable.…
Oscillatory gene circuits are ubiquitous to biology and are involved in fundamental processes of cell cycle, circadian rhythms and developmental systems. The synthesis of small, non-natural oscillatory genetic circuits have been…
Methylation of CpG dinucleotides is a prevalent epigenetic modification that is required for proper development in vertebrates, and changes in CpG methylation are essential to cellular differentiation. Genome-wide DNA methylation assays…
The methylation of DNA regulates gene expression. On cell division the methylation state of the DNA is typically inherited from parent to daughter cells. While the chemical bond between the methyl group and the DNA is very strong, changes…
The spiking properties of a subcritical Hopf oscillator with a time delayed nonlinear feedback is investigated. Finite time delay is found to significantly affect both the statistics and the fine structure of the spiking behavior. These…
We demonstrate the advantages of feedforward loops using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical behaviors of network embedded feedback and…
The circadian clock can adapt itself to external cues, but the molecular mechanisms and regulatory networks governing circadian oscillations' transient adjustments are still largely unknown. Here we consider the specific case of circadian…