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We introduce concepts from optimal estimation to the stabilization of precision frequency standards limited by noisy local oscillators. We develop a theoretical framework casting various measures for frequency standard variance in terms of…
The dynamics of qubits coupled to a harmonic oscillator with time-periodic coupling is investigated in the framework of Floquet theory. This system can be used to model nonadiabatic phenomena that require a periodic modulation of the…
Genetic algorithms are a well-known example of bio-inspired heuristic methods. They mimic natural selection by modeling several operators such as mutation, crossover, and selection. Recent discoveries about Epigenetics regulation processes…
In a recent series of ground-breaking experiments, Nakajima et al. [Science 308, 414-415 (2005)] showed that the three cyanobacterial clock proteins KaiA, KaiB, and KaiC are sufficient in vitro to generate circadian phosphorylation of KaiC.…
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…
Networks of globally coupled, noise activated, bistable elements with connection time delays are considered. The dynamics of these systems is studied numerically using a Langevin description and analytically using (1) a Gaussian…
We systematically investigate the phenomena of coherence resonance in time-delay coupled networks of FitzHugh-Nagumo elements in the excitable regime. Using numerical simulations, we examine the interplay of noise, time-delayed coupling and…
Epigenome modulation in response to the environment potentially provides a mechanism for organisms to adapt, both within and between generations. However, neither the extent to which this occurs, nor the molecular mechanisms involved are…
Ultradian rhythms - quasi-rhythmic fluctuations in behavior and physiology with periods shorter than 24 hours - are observed across various organisms, including humans. Despite their role in key biological processes such as sleep…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
We study the Hamiltonian Mean Field (HMF) model of coupled Hamiltonian rotors with a heterogeneous distribution of moments of inertia and coupling strengths. We show that when the parameters of the rotors are heterogeneous, finite size…
We study the dynamical regimes demonstrated by a pair of identical 3-element ring oscillators (reduced version of synthetic 3-gene genetic Repressilator) coupled using the design of the "quorum sensing (QS)" process natural for…
Nearly all circadian clocks maintain a period that is insensitive to temperature changes, a phenomenon known as temperature compensation (TC). Yet, it is unclear whether there is any common feature among different systems that exhibit TC.…
Many biological oscillators are arranged in networks composed of many inter-coupled cellular oscillators. However, results are still lacking on the collective oscillation period of inter-coupled gene regulatory oscillators, which, as has…
We study Nielsen's circuit complexity in a periodic harmonic oscillator chain, under single and multiple quenches. In a multiple quench scenario, it is shown that the complexity shows remarkably different behaviour compared to the other…
The maintainance of a stable periodicity during the yeast metabolic cycle involving approximately half of the genome requires a very strict and efficient control of gene expression. For this reason, the metabolic cycle is a very good…
We investigate the creation and control of emergent collective behavior and quantum correlations using feedback in an emitter-waveguide system using a minimal model. Employing homodyne detection of photons emitted from a laser-driven…
A number of biological rhythms originate from networks comprised of multiple cellular oscillators. But analytical results are still lacking on the collective oscillation period of inter-coupled gene regulatory oscillators, which, as has…
Building upon our previous work on the Wilson-Cowan equations with distributed delays, we study the dynamic behavior in a system of two coupled Wilson-Cowan pairs. We focus in particular on understanding the mechanisms that govern the…
We consider the effect of distributed delays in neural feedback systems. The avian optic tectum is reciprocally connected with the nucleus isthmi. Extracellular stimulation combined with intracellular recordings reveal a range of signal…