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There are three ways to conceptualize entropy: entropy as an extensive thermodynamic quantity of physical systems (Clausius, Boltzmann, Gibbs), entropy as a measure for information production of ergodic sources (Shannon), and entropy as a…

We investigate the nonequilibrium stationary states of systems consisting of chemical reactions among molecules of several chemical species. To this end we introduce and develop a stochastic formulation of nonequilibrium thermodynamics of…

Chemical and biological networks can describe a wide variety of processes, from gene regulatory networks to biochemical oscillations. Modeled by chemical master equations, these processes are inherently stochastic, as fluctuations dominate…

The thermodynamic definition of entropy can be extended to nonequilibrium systems based on its relation to information. To apply this definition in practice requires access to the physical system's microstates, which may be prohibitively…

Stochastic thermodynamics is formulated under the assumption of perfect knowledge of all thermodynamic parameters. However, in any real-world experiment, there is non-zero uncertainty about the precise value of temperatures, chemical…

We put forth a unifying formalism for the description of the thermodynamics of continuously monitored systems, where measurements are only performed on the environment connected to a system. We show, in particular, that the conditional and…

We investigate the thermodynamics as well as the population dynamics of ecosystems based on a stochastic approach in which the number of individuals of the several species of the ecosystem are treated as stochastic variables. The several…

The theoretical understanding of active matter, which is driven out of equilibrium by directed motion, is still fragmental and model oriented. Stochastic thermodynamics, on the other hand, is a comprehensive theoretical framework for driven…

We present the stochastic thermodynamics analysis of an open quantum system weakly coupled to multiple reservoirs and driven by a rapidly oscillating external field. The analysis is built on a modified stochastic master equation in the…

Markedly increased computational power and data acquisition have led to growing interest in data-driven inverse dynamics problems. These seek to answer a fundamental question: What can we learn from time series measurements of a complex…

The past two decades have seen a revolution in statistical physics, generalizing it to apply to systems of arbitrary size, evolving while arbitrarily far from equilibrium. Many of these new results are based on analyzing the dynamics of the…

A central concept in the connection between physics and information theory is entropy, which represents the amount of information extracted from the system by the observer performing measurements in an experiment. Indeed, Jaynes' principle…

Reciprocal relations correlate fairly accurately a great variety of experimental results. Nevertheless, the concepts of statistical fluctuations, and microscopic reversibility - the bases of the accepted proof of the relations by Onsager -…

We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…

Complex systems produce high-dimensional signals that lack macroscopic variables analogous to entropy, temperature, or free energy. This work introduces a thermoinformational formulation that derives entropy, internal energy, temperature,…

We consider a Brownian particle confined by an external potential and subject to stochastic resetting to the origin. Motivated by the repetitive nature of the dynamics, we describe the process as a thermodynamic cycle of thermal expansion…

Depending on the exact experimental conditions, the thermodynamic properties of physical systems can be related to one or more thermostatistical ensembles. Here, we survey the notion of thermodynamic temperature in different statistical…

In these decades, it has been revealed that there is rich information-theoretic structure in thermodynamics of out-of-equilibrium systems in both the classical and quantum regimes. This has led to the fruitful interplay among statistical…

Thermodynamics and information have intricate inter-relations. The justification of the fact that information is physical, is done by inter-linking information and thermodynamics - through Landauer's principle. This modern approach towards…

The second law of thermodynamics implies a relationship between the net entropy export by the Earth and its internal irreversible entropy production. The application of this constraint for the purpose of understanding Earth's climate is…