Related papers: Type-dependent stochastic Ising model describing t…
We describe an approach to model genetic regulatory networks at the level of promotion-inhibition circuitry through a class of stochastic spin models that includes spatial and temporal density fluctuations in a natural way. The formalism…
We introduce and analyze a natural class of nonlinear dynamics for spin systems such as the Ising model. This class of dynamics is based on the framework of mass action kinetics, which models the evolution of systems of entities under…
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…
We study an excitable active rotator with slowly adapting nonlinear feedback and noise. Depending on the adaptation and the noise level, this system may display noise-induced spiking, noise-perturbed oscillations, or stochastic busting. We…
This paper applies the classical prediction error method (PEM) to the estimation of nonlinear discrete-time models of neuronal systems subject to input-additive noise. While the nonlinear system exhibits excitability, bifurcations, and…
Asymmetric Ising model, in which coupled spins affect each other differently, plays an important role in diverse fields, from physics to biology to artificial intelligence. We show that coupled parametric oscillators provide a…
A fast harmonic oscillator is linearly coupled with a system of Ising spins that are in contact with a thermal bath, and evolve under a slow Glauber dynamics at dimensionless temperature $\theta$. The spins have a coupling constant…
To investigate novel aspects of pattern formation in spin systems, we use a mapping between reactive concentrations in a reaction-diffusion system and spin orientations in a dynamic multiple-spin Ising model. While pattern formation in…
We investigate a stochastic approach to non-equilibrium quantum spin systems based on recent insights linking quantum and classical dynamics. Exploiting a sequence of exact transformations, quantum expectation values can be recast as…
Systems with nonreciprocal interactions generically display time-dependent states. These are routinely observed in finite systems, from neuroscience to active matter, in which globally ordered oscillations exist. However, the stability of…
The nonlinear response to an oscillating field is calculated for a kinetic trap model with an exponential density of states and the results are compared to those for the model with a Gaussian density of states. The calculations are limited…
We study the dynamical response of a two-dimensional Ising model subject to a square-wave oscillating external field. In contrast to earlier studies, the system evolves under a so-called soft Glauber dynamic [P.A. Rikvold and M. Kolesik, J.…
Periodic recurrence is a prominent behavioural of many biological phenomena, including cell cycle and circadian rhythms. Although deterministic models are commonly used to represent the dynamics of periodic phenomena, it is known that they…
The analytical description of the dynamics in models with discrete variables (e.g. Ising spins) is a notoriously difficult problem, that can be tackled only under some approximation. Recently a novel variational approach to solve the…
Oscillations in nonequilibrium noisy systems are important physical phenomena. These oscillations can happen in autonomous biochemical oscillators such as circadian clocks. They can also manifest as subharmonic oscillations in periodically…
An ensemble of uncoupled limit-cycle oscillators receiving common Poisson impulses shows a range of non-trivial behavior, from synchronization, desynchronization, to clustering. The group behavior that arises in the ensemble can be…
Biomolecular feedback systems are now a central application area of interest within control theory. While classical control techniques provide invaluable insight into the function and design of both natural and synthetic biomolecular…
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…
We consider an ensemble of coupled nonlinear noisy oscillators demonstrating in the thermodynamic limit an Ising-type transition. In the ordered phase and for finite ensembles stochastic flips of the mean field are observed with the rate…