相关论文: The Repressor-Lattice: Feed-Back, Commensurability…
The genetic repressilator circuit consists of three transcription factors, or repressors, which negatively regulate each other in a cyclic manner. This circuit was synthetically constructed on plasmids in {\it Escherichia coli} and was…
Two synthetic gene circuits -- the genetic toggle switch and the repressilator -- are analyzed quantitatively and discussed in the context of an educational module on gene circuits and feedback that constitutes the final topic of a…
Novel mathematical models of three different repressilator topologies are introduced. As designable transcription factors have been shown to bind to DNA non-cooperatively, we have chosen models containing non-cooperative elements. The…
We analyze three simple genetic circuits which involve transcriptional regulation and feedback: the autorepressor, the switch and the repressilator, that consist of one, two and three genes, respectively. Such systems are commonly simulated…
In 2000, Elowitz and Leibler introduced the repressilator--a synthetic gene circuit with three genes that cyclically repress transcription of the next gene--as well as a corresponding mathematical model. Experimental data and model…
Mixed positive and negative feedback loops are often found in biological systems which support oscillations. In this work we consider a prototype of such systems, which has been recently found at the core of many genetic circuits showing…
Negative and positive transcriptional feedback loops are present in natural and synthetic genetic oscillators. A single gene with negative transcriptional feedback needs a time delay and sufficiently strong nonlinearity in the transmission…
We study, numerically and analytically, the stability of synchronization for an ensemble of coupled phase oscillators with attractive and repulsive interactions, as a function of the number of repulsive couplings and their intensity.…
Genetic oscillators play important roles in cell life regulation. The regulatory efficiency usually depends strongly on the emergence of stable collective dynamic modes, which requires designing the interactions between genetic networks. We…
A family of repressor networks is proposed as a simple model of gene regulatory networks. We analytically show three topological classes of the repressor networks, each of which exhibits distinctly growing complexity of spatiotemporal…
The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule…
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by rational design of the reaction network, and using existing…
The simplest ring oscillator is made from three strongly nonlinear elements repressing each other unidirectionally resulting in the emergence of a limit cycle. A popular implementation of this scheme uses repressive genes in bacteria…
Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available…
Two-dimensional Josephson junction arrays frustrated by a perpendicular magnetic field are predicted to form a cascade of distinct vortex lattice states. Here, we show that the resistivity tensor provides both structural and dynamical…
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…
Phasor Agents are dynamical systems whose internal state is a Phasor Graph: a weighted graph of coupled Stuart-Landau oscillators. A Stuart-Landau oscillator is a minimal stable "rhythm generator" (the normal form near a Hopf bifurcation);…
Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behavior in…
A coarse grained description of a two-dimensional prey-predator system is given in terms of a 3-state lattice model containing two control parameters: the spreading rates of preys and predators. The properties of the model are investigated…
We study a model for itinerant, strongly interacting fermions where a judicious tuning of the interactions leads to a supersymmetric Hamiltonian. On the triangular lattice this model is known to exhibit a property called superfrustration,…