Related papers: Quantifying dissipation in stochastic complex osci…
We consider stochastic rotational dynamics of a macrospin at a constant temperature, in presence of an external magnetic field. Starting from the appropriate Langevin equation which contains multiplicative noise, we calculate entropy…
The brain is a non-equilibrium system whose dynamics change in different brain states, such as wakefulness and deep sleep. Thermodynamics provides the tools for revealing these non-equilibrium dynamics. We used violations of the…
The selection of an equilibrium state by maximising the entropy of a system, subject to certain constraints, is often powerfully motivated as an exercise in logical inference, a procedure where conclusions are reached on the basis of…
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…
Stochastic thermodynamics of chemical reaction systems has recently gained much attention. In the present paper, we consider such an issue for a system with both oscillatory and excitable dynamics, using catalytic oxidation of carbon…
Studying the structure of systems in nonequilibrium steady states necessitates tools that quantify population shifts and associated deformations of equilibrium free energy landscapes under persistent currents. Within the framework of…
A number of biological systems can be modeled by Markov chains. Recently, there has been an increasing concern about when biological systems modeled by Markov chains will perform a dynamic phenomenon called overshoot. In this article, we…
The developing field of stochastic thermodynamics extends concepts of macroscopic thermodynamics such as entropy production and work to the microscopic level of individual trajectories taken by a system through phase space. The scheme…
Predicting how systems respond to external perturbations far from equilibrium remains a fundamental challenge across physics, chemistry, and biology. We present a unified response framework for stochastic Markov dynamics that integrates…
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 develop the stochastic approach to thermodynamics based on the stochastic dynamics, which can be discrete (master equation) continuous (Fokker-Planck equation), and on two assumptions concerning entropy. The first is the definition of…
We investigate the oscillatory dynamics and bifurcation structure of a reaction-diffusion system with bistable nonlinearity and mass conservation, which was proposed by [Otsuji et al, PLoS Comp. Biol. 3 (2007), e108]. The system is a useful…
Using equilibrium fluctuations to understand the response of a physical system to an externally imposed perturbation is the basis for linear response theory, which is widely used to interpret experiments and shed light on microscopic…
We study the nonequilibrium dynamics of photoinduced phase transitions in charge ordered (CO) systems with a strong electron-lattice interaction and analyze the interplay between electrons, periodic lattice distortions, and a phonon thermal…
A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…
We show that for stochastic dynamical systems out of equilibrium the violation of the fluctuation-dissipation equality is bounded by a function of the entropy production. The result applies to a much wider situation than `near equilibrium',…
We study the non-equilibrium dissipative dynamics of the center of mass of a particle coupled to a field via its internal degrees of freedom. We model the internal and external degrees of freedom of the particle as quantum harmonic…
Cellular Potts models are broadly applied across developmental biology and cancer research. We overcome limitations of the traditional approach, which reinterprets a modified Metropolis sampling as ad hoc dynamics, by introducing a physical…
Accurate predictions of charge excitation energies of molecules in the disordered condensed phase are central to the chemical reactivity, stability, and optoelectronic properties of molecules and critically depend on the specific…
Systems coupled to multiple thermodynamic reservoirs can exhibit nonequilibrium dynamics, breaking detailed balance to generate currents. To power these currents, the entropy of the reservoirs increases. The rate of entropy production, or…