Related papers: Oscillation in microRNA Feedback Loop
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
Both short interfering RNAs (siRNAs) and microRNAs (miRNAs) mediate the repression of specific sequences of mRNA through the RNA interference pathway. In the last years several experiments have supported the hypothesis that siRNAs and…
We propose a statistical model of a large random network with high connectivity in order to describe the behavior of {\it E.\,coli} cells after exposure to acute stress. The building blocks of this network are feedback cycles typical of the…
We report the first measurements of the intrinsic strain fluctuations of living cells using a recently-developed tracer correlation technique along with a theoretical framework for interpreting such data in heterogeneous media with…
Adaptation to environmental change is a common property of biological systems. Cells initially respond to external changes in the environment, but after some time, they regain their original state. By considering an element consisting of…
Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where a gene regulates its own expression. The nonlinear coupling…
Neural oscillations are electrical activities of the brain measurable at different frequencies. This paper studies the interaction between the fast and slow processes in the brain. We recorded signals intracranially from the simple Wistar…
We numerically investigate the stress distribution of a paste when an external oscillation is applied. The paste memorizes the oscillation as plastic deformation. Due to the plastic deformation, the residual stress remains after the…
MicroRNA-mediated regulation of gene expression is characterised by some distinctive features that set it apart from unregulated and transcription factor-regulated gene expression. Recently, a mathematical model has been proposed to…
The short-term memory effects recently observed in vibration-induced compaction of granular materials are studied. It is shown that they can be explained by means of quite plausible hypothesis about the mesoscopic description of the…
Simple models of clarinet instruments based on iterated maps have been used in the past to successfully estimate the threshold of oscillation of this instrument as a function of a constant blowing pressure. However, when the blowing…
Feedback loops are essential for regulating cell proliferation and maintaining the delicate balance between cell division and cell death. Thanks to the exact solution of a few simple models of cell growth it is by now clear that stochastic…
We analyze a class of network motifs in which a short, two-node positive feed- back motif is inserted in a three-node negative feedback loop. We demonstrate that such networks can undergo a bifurcation to a state where a stable fixed point…
MicroRNAs are small noncoding RNAs that regulate genes post-transciptionally by binding and degrading target eukaryotic mRNAs. We use a quantitative model to study gene regulation by inhibitory microRNAs and compare it to gene regulation by…
Several studies highlighted the relevance of extrinsic noise in shaping cell decision making and differentiation in molecular networks. Experimental evidences of phenotypic differentiation are given by the presence of bimodal distributions…
We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a…
Oscillations lie at the core of many biological processes, from the cell cycle, to circadian oscillations and developmental processes. Time-keeping mechanisms are essential to enable organisms to adapt to varying conditions in environmental…
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…
The study of the response of amorphous materials to oscillatory strain is traditionally performed with many repeated cycles. We argue that it pays to consider carefully just one cycle (and may be a second), to reveal the rich physics that…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…