Related papers: Time-delayed model of RNA interference
Small interfering RNA (siRNA) is a short double-stranded RNA molecule (about 21-23 nucleotides) with the potential to cure diseases by silencing the function of target genes. Due to its well-understood mechanism, many siRNA-based drugs have…
Understanding dynamics of an infectious disease helps in designing appropriate strategies for containing its spread in a population. Recent mathematical models are aimed at studying dynamics of some specific types of infectious diseases. In…
Regulation of intrinsic noise in gene expression is essential for many cellular functions. Correspondingly, there is considerable interest in understanding how different molecular mechanisms of gene expression impact variations in protein…
Discrete-time systems under aperiodic sampling may serve as a modeling abstraction for a multitude of problems arising in cyber-physical and networked control systems. Recently, model- and data-based stability conditions for such systems…
We investigate the dynamics of a single breathing localized structure in a three-component reaction-diffusion system subjected to the time-delayed feedback. We show that variation of the delay time and the feedback strength can lead either…
We propose a paradigmatic model system, a subcritical Hopf normal form subjected to noise and time-delayed feedback, to investigate the impact of time delay on coherence resonance in non-excitable systems. We develop analytical tools to…
Single cell experiments of simple regulatory networks can markedly differ from cell population experiments. Such differences arise from stochastic events in individual cells that are averaged out in cell populations. For instance, while…
RNA velocity is an important model that combines cellular spliced and unspliced RNA counts to infer dynamical properties of various regulatory functions. Despite its wide applicability and many variants used in practice, the model has not…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
Almost all viruses, regardless of their genomic material, produce defective viral genomes (DVG) as an unavoidable byproduct of their error-prone replication. Defective interfering (DI) elements are a subgroup of DVGs that have been shown to…
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…
When analysing gene expression time series data an often overlooked but crucial aspect of the model is that the regulatory network structure may change over time. Whilst some approaches have addressed this problem previously in the…
We show that non-steric molecular interactions between RNA polymerase (RNAP) motors that move simultaneously on the same DNA track determine strongly the kinetics of transcription elongation. With a focus on the role of collisions and…
We study theoretically a bistable systems with time-delayed feedback driven by weak periodic force. The effective potential function and the steady-state probability density are derived. The delay time and the strength of its feedback can…
A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such…
Chemical reactions in cell are subject to intense stochastic fluctuations. An important question is how the fundamental physiological behavior of cell is kept stable against those noisy perturbations. In this paper a stochastic model of…
Using the model of a generalized Van der Pol oscillator in the regime of subcritical Hopf bifurcation we investigate the influence of time delay on noise-induced oscillations. It is shown that for appropriate choices of time delay either…
Active agents with time-delayed interactions arise naturally in various real-world systems, such as biological systems, transportation networks and robotic swarms. Such systems are typically modeled as Delay Differential Equations (DDEs)…