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Biochemical oscillations are ubiquitous in nature and allow organisms to properly time their biological functions. In this paper, we consider minimal Markov state models of nonequilibrium biochemical networks that support oscillations. We…
We employ an equivalent-circuit model of a multi-cell cavity to explore its time-dependent behavior in order to understand differences between the multi-cell model and the commonly-used model of a single-cell resonator. Furthermore, we…
Bosonic encoding is an approach for quantum information processing, promising lower hardware overhead by encoding in the many levels of a harmonic oscillator mode. Scaling to multiple modes requires weak interaction for independent control,…
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…
This paper generalizes recent results by the authors on noninvasive model-reference adaptive control designs for control-based continuation of periodic orbits in periodically excited linear systems with matched uncertainties to a larger…
Motivated by the observation of non-exponential run-time distributions of bacterial swimmers, we propose a minimal phenomenological model for taxis of active particles whose motion is controlled by an internal clock. The ticking of the…
Systems with the coexistence of different stable attractors are widely exploited in systems biology in order to suitably model the differentiating processes arising in living cells. In order to describe genetic regulatory networks several…
We investigate a driven, one-dimensional system of colloidal particles in a periodically currogated narrow channel subject to a time-delayed feedback control. Our goal is to identify conditions under which the control induces oscillatory,…
Oscillatory gene circuits are ubiquitous to biology and are involved in fundamental processes of cell cycle, circadian rhythms and developmental systems. The synthesis of small, non-natural oscillatory genetic circuits have been…
A composite, exponential relaxation function, modulated by a periodic component, was used to fit to an experimental time series of blood glucose levels. The 11 parameters function that allows for the detection of a possible rhythm…
The main objective of quantum simulation is an in-depth understanding of many-body physics. It is important for fundamental issues (quantum phase transitions, transport, . . . ) and for the development of innovative materials. Analytic…
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported…
Reservoir computing is a machine learning framework that uses artificial or physical dissipative dynamics to predict time-series data using nonlinearity and memory properties of dynamical systems. Quantum systems are considered as promising…
We propose a new dynamical method to connect equilibrium quantum phase transitions and quantum coherence using out-of-time-order correlations (OTOCs). Adopting the iconic Lipkin-Meshkov-Glick and transverse-field Ising models as…
We have studied theoretically the basic operation of a quantum feedback loop designed to maintain the desired phase of quantum coherent oscillations in a two-level system. Such feedback can suppress the dephasing of oscillations due to…
We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under1 quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady…
Classically integrable approximants are here constructed for a family of predominantly chaotic periodic systems by means of the Baker-Hausdorff-Campbell formula. We compare the evolving wave density for the corresponding exact quantum…
In genomic applications, there is often interest in identifying genes whose time-course expression trajectories exhibit periodic oscillations with a period of approximately 24 hours. Such genes are usually referred to as circadian, and…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Finite systems of bosons and/or fermions described by the Hubbard model can be realized using ultracold atoms confined in optical lattices. The ground states of these systems often exhibit a coexistence of compressible superfluid and…