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The bistable gene regulatory switch controlling the transition from lysogeny to lysis in bacteriophage lambda presents a unique challenge to quantitative modeling. Despite extensive characterization of this regulatory network, the origin of…
We propose a new non-equilibrium model for spatial pattern formation on the basis of local information transfer. Unlike standard models of pattern formation it is not based on the Turing instability. Information is transmitted through the…
Clonal microbes can switch between different phenotypes and recent theoretical work has shown that stochastic switching between these subpopulations can stabilize microbial communities. This phenotypic switching need not be stochastic,…
It was observed in recent experiments that the current-voltage characteristics (IV) of BPDN-DT (bipyridyl- dinitro- oligophenylene- ethynylene- dithiol) can be switched in a very controlled manner between "on" and "off" traces by applying a…
Robust oscillations play crucial roles in a wide variety of biological processes and are often generated by deterministic mechanisms. However, stochastic fluctuations often generate complex perturbations of these deterministic oscillations,…
Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. Signatures of regime shifts in gene…
In this work, we present the effects of stochastic force generated by white noise on the nonlinear dynamics of a circular silicon nitride membrane. By tuning the membrane to the Duffing nonlinear region, detected signals switching between…
Biological systems are majorly dependent on their property of bistability in order to exhibit nongenetic heterogeneity in terms of cellular morphology and physiology. Spatial patterns of phenotypically heterogeneous cells, arising due to…
We examine a spatially discrete reaction diffusion model based on the interactions that create a periodic pattern in the Drosophila eye imaginal disc. This model is capable of generating a regular hexagonal pattern of gene expression behind…
In contrast to the static operations of conventional semiconductor devices, the dynamic conformational freedom in molecular devices opens up the possibility of using molecules as new types of devices such as a molecular conformational…
We consider an epidemiological model that includes waning and boosting of immunity. Assuming that repeated exposure to the pathogen fully restores immunity, we derive an SIRS-type model with discrete and distributed delays. First we prove…
NF-{\kappa}B is a pleiotropic protein whose nucleo-cytoplasmic trafficking is tightly regulated by multiple negative feedback loops embedded in the NF-{\kappa}B signaling network and contributes to diverse gene expression profiles important…
Positive feedback and cooperativity in the regulation of gene expression are generally considered to be necessary for obtaining bistable expression states. Recently, a novel mechanism of bistability termed emergent bistability has been…
The effects of intrinsic noise on stochastic delay systems is studied within an expansion in the inverse system size. We show that the stochastic nature of the underlying dynamics may induce oscillatory behaviour in parameter ranges where…
Biological systems encode function not primarily in steady states, but in the structure of transient responses elicited by time-varying stimuli. Overshoots, biphasic dynamics, adaptation kinetics, fold-change detection, entrainment, and…
We use inelastic hard sphere molecular dynamics simulations and laboratory experiments to study patterns in vertically oscillated granular layers. The simulations and experiments reveal that {\em phase bubbles} spontaneously nucleate in the…
Recent research discovered that charge transfer processes in chiral molecules can be spin selective and named the effect chiral-induced spin selectivity (CISS). Follow-up work studied hybrid spintronic devices with conventional electronic…
Current-voltage characteristics of resonant-tunneling structures often exhibit intrinsic bistabilities. In the bistable region of the I-V curve one of the two current states is metastable. The system switches from the metastable state to…
Cells use genetic switches to shift between alternate gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Here, we study the dynamics of switching in a generic-feedback on/off switch. Unlike…
A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. In this…