Related papers: Time-delayed model of RNA interference
Signal duration (e.g. the time scales over which an active signaling intermediate persists) is a key regulator of biological decisions in myriad contexts such as cell growth, proliferation, and developmental lineage commitments.…
Genetically engineered bacteria to increase the tumbling frequency of the run-and-tumble motion for the higher local bacterial density form visible stripe pattern composed of successive high and low density regions on an agar plate. We…
Suspensions of elongated micelles under shear display complex non-linear behaviour including shear banding, spatio-temporal oscillatory patterns and chaotic response. Based on a suitable rheological model [S. M. Fielding and P. D. Olmsted,…
Contamination by Radio Frequency Interference (RFI) is a ubiquitous challenge for radio astronomy. In particular, transient RFI is difficult to detect and avoid, especially in large data sets with many time bins. In this work, we present a…
How patterns and structures undergo symmetry breaking and self-organize within biological systems from initially homogeneous states is a key issue for biological development. The activator-inhibitor (AI) mechanism, derived from…
In fast growing bacteria, ribosomal RNA (rRNA) is required to be transcribed at very high rates to sustain the high cellular demand on ribosome synthesis. This results in dense traffic of RNA polymerases (RNAP). We developed a stochastic…
A nonlinear time-delay model is proposed to describe the interaction dynamics between criminal and non-criminal populations, combining social influence mechanisms, saturation effects represented by a Holling type II functional response, and…
We consider the stochastic patterns of a system of communicating, or coupled, self-propelled particles in the presence of noise and communication time delay. For sufficiently large environmental noise, there exists a transition between a…
MicroRNAs (miRNAs) critically modulate stem cell properties like pluripotency, but the fundamental mechanism remains largely unknown. This study systematically analyzes multiple-omics data and builds a systems physical network including…
Gene expression is a fundamental process in a living system. The small RNAs (sRNAs) is widely observed as a global regulator in gene expression. The inherent nonlinearity in this regulatory process together with the bursty production of…
We build a simple model for feedback systems involving small RNA (sRNA) molecules based on the iron metabolism system in the bacterium E. coli, and compare it with the corresponding system in H. pylori which uses purely transcriptional…
Regulation of mRNA decay is a critical component of global cellular adaptation to changing environments. The corresponding changes in mRNA lifetimes can be coordinated with changes in mRNA transcription rates to fine-tune gene expression.…
Interference alignment (IA) is a cooperative transmission strategy that improves spectral efficiency in high signal-to-noise ratio (SNR) environments, yet performs poorly in low-SNR scenarios. This limits IA's utility in cellular systems as…
Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction…
We present a linear model, which mimics the response of a spatially extended dissipative medium to a distant perturbation, and investigate its dynamics under delayed feedback control. The time a perturbation needs to propagate to a…
A wide range of organisms use circadian clocks to keep internal sense of daily time and regulate their behavior accordingly. Most of these clocks use intracellular genetic networks based on positive and negative regulatory elements. The…
The expansion of inverter-connected generation facilities (i.e. wind and photovoltaics) and the removal of conventional power plants is necessary to mitigate the impacts of climate change. Whereas conventional generation with large rotating…
In this paper we study an important global regulation mechanism of transcription of biological cells using specific macro-molecules, 6S RNAs. The functional property of 6S RNAs is of blocking the transcription of RNAs when the environment…
According to the `ceRNA hypothesis', microRNAs (miRNAs) may act as mediators of an effective positive interaction between long coding or non-coding RNA molecules, carrying significant potential implications for a variety of biological…
We study the effects of noise on the dynamics of a system of coupled self-propelling particles in the case where the coupling is time-delayed, and the delays are discrete and randomly generated. Previous work has demonstrated that the…