Related papers: Oscillation in microRNA Feedback Loop
microRNAs (miRNAs) regulate gene expression at post-transcriptional level by repressing target RNA molecules. Competition to bind miRNAs tends in turn to correlate their targets, establishing effective RNA-RNA interactions that can…
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…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
We model unzipping of DNA/RNA molecules subject to an external force by a spin-oscillator system. The system comprises a macroscopic degree of freedom, represented by a one-dimensional oscillator, and internal degrees of freedom,…
Traditional percolation theory assumes static microscopic rules, limiting its ability to describe real-world complex systems where macroscopic order actively regulates local interactions. Here, we introduce feedback percolation, an unified…
Transcriptional pulsing has been observed in both prokaryotes and eukaryotes and plays a crucial role in cell to cell variability of protein and mRNA numbers. The issue is how the time constants associated with episodes of transcriptional…
Subthreshold oscillations in neurons are those oscillations which do not attain the critical value of the membrane's voltage needed for triggering an action potential (a spike). Their contribution to the forming of action potentials in…
Infectious diseases often involve multiple strains that interact through the immune response generated after an infection. This study investigates the conditions under which a two-strain epidemic model with partial cross-immunity can lead…
Many neuronal systems and models display a certain class of mixed mode oscillations (MMOs) consisting of periods of small amplitude oscillations interspersed with spikes. Various models with different underlying mechanisms have been…
According to the `ceRNA hypothesis', microRNAs (miRNAs) may act as mediators of an effective positive interaction between long coding or non-coding RNA molecules, carrying significant potential implications for a variety of biological…
Biopolymer looping is a dynamic process that occurs ubiquitously in cells for gene regulation, protein folding, etc. In cellular environments, biopolymers are often subject to tensions which are either static, or temporally fluctuating far…
In this paper we use a continuous model to describe the development of a single cell lineage following the committal of stem cells. Three separate controls are implemented in the model, namely the proliferative control of stem cells, the…
The observation that, through a titration mechanism, microRNAs (miRNAs) can act as mediators of effective interactions among their common targets (competing endogenous RNAs or ceRNAs) has brought forward the idea ('ceRNA hypothesis') that…
Kink oscillations of coronal loops, i.e., standing kink waves, is one of the most studied dynamic phenomena in the solar corona. The oscillations are excited by impulsive energy releases, such as low coronal eruptions. Typical periods of…
The presence of both critical behavior and oscillating patterns in brain dynamics is a very interesting issue. In this paper, we consider a model for a neuron population, where each neuron is modeled by an over-damped rotator. We find that…
Microbial populations in the natural environment are likely to experience growth conditions very different from those of a typical laboratory xperiment. In particular, removal rates of biomass and substrate are unlikely to be balanced under…
Active phenomena which involve force generation and motion play a key role in a number of phenomena in living cells such as cell motility, muscle contraction and the active transport of material and organelles. Here we discuss mechanical…
The oscillatory response of nonlinear systems exhibits characteristic phenomena such as multistability, discontinuous jumps and hysteresis. These can be utilized in applications leading, e.g., to precise frequency measurement, mixing,…
We study in detail the recent suggestions by Tshiprut et al. [Phys. Rev. Lett. 95, 016101 (2005)] to tune tribological properties at the nanoscale by subjecting a substrate to periodic mechanical oscillations. We show that both in…
We build a simple model for feedback systems involving small RNA (sRNA) molecules based on the iron metabolism system in the bacterium E. coli, and compare it with the corresponding system in H. pylori which uses purely transcriptional…