Related papers: Time-delayed model of RNA interference
Noise has significant impact on nonlinear phenomena. Here we demonstrate that, in opposition to previous assumptions, additive noise interfere with the linear stability of scalar nonlinear systems when these are subject to time delay. We…
We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large…
We propose here a stochastic binary element whose transition rate depends on its state at a fixed interval in the past. With this delayed stochastic transition this is one of the simplest dynamical models under the influence of ``noise''…
Various field and laboratory experiments show that prey refuge plays a significant role in the stability of prey-predator dynamics. On the other hand, theoretical studies show that delayed system exhibits a much more realistic dynamics than…
Recent experiments showed that multiple copies of the molecular machine RNA polymerase (RNAP) can efficiently synthesize mRNA collectively in the active state of the promoter. However, environmentally-induced promoter repression results in…
In this paper, we focus on the synthesis of secure timed systems which are modelled as timed automata. The security property that the system must satisfy is a non-interference property. Intuitively, non-interference ensures the absence of…
We analyze the stabilization of unstable steady states by delayed feedback control with a periodic time-varying delay in the regime of a high-frequency modulation of the delay. The average effect of the delayed feedback term in the control…
In this paper, a mathematical model of pneumococcal pneumonia with time delays is proposed. The stability theory of delay differential equations is used to analyze the model. The results show that the disease-free equilibrium is…
Current biological AI models lack interpretability -- their internal representations do not correspond to biological relationships that researchers can examine. Understanding gene regulation requires models whose learned structure can be…
Many transcription factors bind to DNA with a remarkable lack of specificity, so that regulatory binding sites compete with an enormous number of non-regulatory 'decoy' sites. For an auto-regulated gene, we show decoy sites decrease noise…
Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are…
This study investigates how the interaction between gene expression time delay and domain size governs spatio-temporal pattern formation in a reaction-diffusion system. To investigate these phenomena, we utilize a modified version of the…
Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcripion factors should explain the different…
We study the control of noise-induced spatio-temporal current density patterns in a semiconductor nanostructure (double barrier resonant tunnelling diode) by multiple time-delayed feedback. We find much more pronounced resonant features of…
Connected radio interferometers are sometimes used in the tied-array mode: signals from antenna elements are coherently added and the sum signal applied to a VLBI backend or pulsar processing machine. Usually there is no computer-controlled…
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…
The main purpose of this paper is to provide a summary of the fundamental methods for analyzing delay differential equations arising in biology and medicine. These methods are employed to illustrate the effects of time delay on the behavior…
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…
Mathematical modeling based on time-delay differential equations is an important tool to study the role of delay in biological systems and to evaluate its impact on the asymptotic behavior of their dynamics. Delays are indeed found in many…
Background: In Escherichia coli, overlapping rounds of DNA replication allow the bacteria to double in faster times than the time required to copy the genome. The precise timing of initiation of DNA replication is determined by a regulatory…