Related papers: Time-delayed model of RNA interference
The processes, resulting in the transcription of RNA, are intrinsically noisy. It was observed experimentally that the synthesis of mRNA molecules is driven by short, burst-like, events. An accurate prediction of the protein level often…
RNA polymerase (RNAP) is molecular machine that polymerizes a RNA molecule, a linear heteropolymer, using a single stranded DNA (ssDNA) as the corresponding template; the sequence of monomers of the RNA is dictated by that of monomers on…
Small, non-coding RNAs (sRNAs) play important roles as genetic regulators in prokaryotes. sRNAs act post-transcriptionally via complementary pairing with target mRNAs to regulate protein expression. We use a quantitative approach to compare…
RNAs are negatively charged molecules residing in macromolecular crowding cellular environments. Macromolecular confinement can influence the ion effects in RNA folding. In this work, using the recently developed tightly bound ion model for…
Urea titration of RNA by urea is an effective approach to investigate the forces stabilizing this biologically important molecule. We used all atom molecular dynamics simulations using two urea force fields and two RNA constructs to…
In the context of the Laser Interferometer Space Antenna (LISA), the laser subsystems exhibit frequency fluctuations that introduce significant levels of noise into the measurements, surpassing the gravitational wave signal by several…
Delays and stochasticity have both served as crucially valuable ingredients in mathematical descriptions of control, physical, and biological systems. In this work, we investigate how explicitly dynamical stochasticity in delays modulates…
This study examines the complex interplay between inertia and time delay in regular rotor networks within the framework of the second-order Kuramoto model. By combining analytical and numerical methods, we demonstrate that intrinsic time…
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…
Time lags are ubiquitous in biophysiological processes and more generally in real-world complex networks. It has been recently proposed to use information-theoretic tools such as transfer entropy to detect and estimate a possible delay in…
A ferrofluid droplet confined in a Hele-Shaw cell can be deformed into a stably spinning ``gear,'' using crossed magnetic fields. Previously, fully nonlinear simulation revealed that the spinning gear emerges as a stable traveling wave…
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…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
Time--delayed feedback is exploited for controlling noise--induced motion in coherence resonance oscillators. Namely, under the proper choice of time delay, one can either increase or decrease the regularity of motion. It is shown that in…
The stability and convergence of the neural networks are the fundamental characteristics in the Hopfield type networks. Since time delay is ubiquitous in most physical and biological systems, more attention is being made for the delayed…
Time delay is ubiquitous in many experimental and real-world situations. It is often unclear whether time delay plays a significant role in observed phenomena, and if it does, how long the time lag really is. This would be invaluable…
A delayed differential equation modelling a single neuron with inertial term is considered in this paper. Hopf bifurcation is studied by using the normal form theory of retarded functional differential equations. When adopting a…
We consider an epidemiological model that includes waning and boosting of immunity. Assuming that repeated exposure to the pathogen fully restores immunity, we derive an SIRS-type model with discrete and distributed delays. First we prove…
Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…
It has recently been suggested that the competition for a finite pool of microRNAs (miRNA) gives rise to effective interactions among their common targets (competing endogenous RNAs or ceRNAs) that could prove to be crucial for…