Related papers: A core genetic module : the Mixed Feedback Loop
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 transcription factors should explain the…
Synchronous neural activity can improve neural processing and is believed to mediate neuronal interaction by providing temporal windows during which information is more easily transferred. We demonstrate a pulse gating mechanism in a…
The Ribosome Flow Model (RFM) describes the unidirectional movement of interacting particles along a one-dimensional chain of sites. As a site becomes fuller, the effective entry rate into this site decreases. The RFM has been used to model…
This paper presents an intracellular feedback control strategy, to regulate the gene expression process dynamics. For this purpose, two types of genetic circuits are designed in order to compare concentrations of the input transcription…
A novel framework for closed-loop control of turbulent flows is tested in an experimental mixing layer flow. This framework, called Machine Learning Control (MLC), provides a model-free method of searching for the best function, to be used…
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…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
We investigate a coherent nonlinear feedback circuit constructed from pre-existing superconducting microwave devices. The network exhibits emergent bistable and astable states, and we demonstrate its operation as a latch and the frequency…
Oscillatory behavior is ubiquitous in many natural and engineered systems, often emerging through self-regulating mechanisms. In this paper, we address the challenge of stabilizing a desired oscillatory pattern in a networked system where…
Delay is an inherent feature of genetic regulatory networks. It represents the time required for the assembly of functional regulator proteins. The protein production process is complex, as it includes transcription, translocation,…
The effect of signal integration through cis-regulatory modules (CRMs) on synchronization and clustering of populations of two-component genetic oscillators coupled by quorum sensing is in detail investigated. We find that the CRMs play an…
We present a design framework to induce stable oscillations through mixed feedback control. We provide conditions on the feedback gain and on the balance between positive and negative feedback contributions to guarantee robust oscillations.…
Mixed feedback loops combining transcriptional and post-transcriptional regulations are common in cellular regulatory networks. They consist of two genes, encoding a transcription factor and a small non-coding RNA (sRNA), which mutually…
The paper highlights the role of a positive feedback gating mechanism at the cellular level in the robust- ness and modulation properties of rhythmic activities at the circuit level. The results are presented in the context of half-center…
Auto-regulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic…
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that…
A wide range of organisms features molecular machines, circadian clocks, which generate endogenous oscillations with ~24 h periodicity and thereby synchronize biological processes to diurnal environmental fluctuations. Recently, it has…
We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…