Related papers: Oscillation in microRNA Feedback Loop
We present a practical method to obtain bounds for the oscillation minima and maxima of large classes of biochemical oscillator models that generate oscillations through a negative feedback. These bounds depend on the feedback nonlinearity…
Biochemical oscillations are ubiquitous in nature and allow organisms to properly time their biological functions. In this paper, we consider minimal Markov state models of nonequilibrium biochemical networks that support oscillations. We…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
The dynamic effects on a magnetic system exposed to a time-oscillating external temperature are studied using Monte Carlo simulations on the classic 2D Ising Model. The time dependence of temperature is defined as $T(t)=T_0 + A \cdot…
The global dynamics of gene regulatory networks are known to show robustness to perturbations in the form of intrinsic and extrinsic noise, as well as mutations of individual genes. One molecular mechanism underlying this robustness has…
A new version of the virtual cathode oscillator, vircator klystron, is suggested and studied numerically. It essentially includes adjustable external feedback. The non-steady-state nonlinear dynamics of the oscillator is analyzed in…
When an interacting many-body system, such as a magnet, is driven in time by an external perturbation, such as a magnetic field,the system cannot respond instantaneously due to relaxational delay. The response of such a system under a…
Reed instruments are modeled as self-sustained oscillators driven by the pressure inside the mouth of the musician. A set of nonlinear equations connects the control parameters (mouth pressure, lip force) to the system output, hereby…
Non-coding RNAs are crucial regulators of gene expression in prokaryotes and eukaryotes, but it remains poorly understood how they affect the dynamics of transcriptional networks. We analyzed the temporal characteristics of the…
Molecular dynamics simulations have been performed to study frictional slip and its influence on energy dissipation and momentum transfer at atomically smooth solid/water interfaces. By modifying surface chemistry, we investigate the…
Social interaction dynamics are a special type of group interactions that play a large part in our everyday lives. They dictate how and with whom a certain individual will interact. One of such interactions can be termed "avoidance…
Transcription commonly occurs in bursts, with alternating productive (ON) and quiescent (OFF) periods, governing mRNA production rates. Yet, how transcription is regulated through bursting dynamics remains unresolved. Here, we conduct…
Fluctuations in the measured mRNA levels of unperturbed cells under fixed conditions have often been viewed as an impediment to the extraction of information from expression profiles. Here, we argue that such expression fluctuations should…
We analyze the governing partial differential equations of a model of pole-to-pole oscillations of the MinD protein in a bacterial cell. The sensitivity to extrinsic noise in the parameters of the model is explored. Our analysis shows that…
It has been recently observed that synthetic materials subjected to an external elastic stress give rise to scaling phenomena in the acoustic emission signal. Motivated by this experimental finding we develop a mesoscopic model in order to…
In this paper, we study through mathematical modelling the combined effect of transcriptional and translational regulation by proteins and small noncoding RNAs (sRNA) in a genetic feedback motif that has an important role in the survival of…
In addition to thermal noise, which is essential to promote conformational transitions in biopolymers, cellular environment is replete with a spectrum of athermal fluctuations that are produced from a plethora of active processes. To…
We study the problem of controlling oscillations in closed loop by combining positive and negative feedback in a mixed configuration. We develop a complete design procedure to set the relative strength of the two feedback loops to achieve…
Cells are known to utilize biochemical noise to probabilistically switch between distinct gene expression states. We demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore…
Fluctuations are inherent to biological systems, arising from the stochastic nature of molecular interactions, and influence various aspects of system behavior, stability, and robustness. These fluctuations can be categorized as intrinsic,…