Related papers: Flexible Dynamics of Two Quorum Sensing Coupled Re…
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…
Engineering genetic networks to be both predictable and robust is a key challenge in synthetic biology. Synthetic circuits must reliably function in dynamic, stochastic and heterogeneous environments, and simple circuits can be studied to…
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 study the effects of multiple binding sites in the promoter of a genetic oscillator. We evaluate the regulatory function of a promoter with multiple binding sites in the absence of cooperative binding, and consider different hypotheses…
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…
Coupled oscillators have been used to study synchronization in a wide range of social, biological, and physical systems, including pedestrian-induced bridge resonances, coordinated lighting up of firefly swarms, and enhanced output peak…
Quantum synchronization (QS) in open many-body systems offers a promising route for controlling collective quantum dynamics, yet existing manipulation schemes often rely on dissipation engineering, which distorts limit cycles, lacks…
Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence…
A regime of coexistence of asynchronous and clustered dynamics is analyzed for globally coupled homogeneous and heterogeneous inhibitory networks of quadratic integrate-and-fire (QIF) neurons subject to Gaussian noise. The analysis is based…
The oscillatory dynamics of natural and man-made systems can be disrupted by their time-varying interactions, leading to oscillation quenching phenomena in which the oscillations are suppressed. We introduce a framework for analyzing,…
This paper reports the analysis of the dynamics of a model of pulse-coupled oscillators with global inhibitory coupling. The model is inspired by experiments on colonies of bacteria-embedded synthetic genetic circuits. The total population…
Networks of coupled dynamical systems provide a powerful way to model systems with enormously complex dynamics, such as the human brain. Control of synchronization in such networked systems has far reaching applications in many domains,…
We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their…
The control of network-coupled nonlinear dynamical systems is an active area of research in the nonlinear science community. Coupled oscillator networks represent a particularly important family of nonlinear systems, with applications…
In this letter, we analyze a genetic toggle switch recently studied in the literature where the expression of two repressor proteins can be tuned by controlling two different inputs, namely the concentration of two inducer molecules in the…
Genetically encoded regulatory circuits control biological function. A major focus of systems biology is to understand these circuits by establishing the relationship between specific structures and functions. Of special interest are…
Collective oscillation of cells in a population has been reported under diverse biological contexts and with vastly different molecular constructs. Could there be common principles similar to those that govern spontaneous oscillation in…
We present the experimental discovery of multiple simultaneous degeneracies in the spectrum of a Kerr oscillator subjected to a squeezing drive. This squeezing, in combination with the Kerr interaction creates an effective static two-well…
In this paper, we delve into the issue of Quantum Synchronization in a driven two-level (qubit) system situated within a structured environment. Our findings have practical implications as we discover that adding a time-dependent periodic…
We investigated the locking behaviors of coupled limit-cycle oscillators with phase and amplitude dynamics. We focused on how the dynamics are affected by inhomogeneous coupling strength and by angular and radial shifts in the coupling…