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We extend the principles of information thermodynamics to study energy and information exchanges between coupled systems composed of one part undergoing a Markov jump process and another underdamped diffusion. We derive integral fluctuation…
We study the dynamic and thermodynamic origin of non-canonical equilibria, and we discuss their connection with the generalized central limit theorem and the micro-canonical Boltzmann principle. We reach the conclusion that the zeroth law…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
Based on a generative model (GM) and beliefs over hidden states, the free energy principle (FEP) enables an agent to sense and act by minimizing a free energy bound on Bayesian surprise. Inclusion of prior beliefs in the GM about desired…
The Principle of Least Action is used with a simple Lagrangian density, involving second-order derivatives of the wave function, to obtain the Schroedinger equation. A Hamiltonian density obtained from this simple Lagrangian density shows…
For binary mixtures of fluids without chemical reactions, but with components having different temperatures, the Hamilton principle of least action is able to produce the equation of motion for each component and a balance equation of the…
Thermodynamic relations are derived from first principles of mechanics for non-equilibrium processes. Since the key role herein is played by the law of increase of entropy, the latter is analyzed at first. It is shown that its derivation…
We further develop a recently introduced variational principle of stationary action for problems in nonconservative classical mechanics and extend it to classical field theories. The variational calculus used is consistent with an initial…
This work extends a recently developed mathematical theory of thermodynamics for Markov processes with, and more importantly, without detailed balance. We show that the Legendre transform in connection to ensemble changes in Gibbs'…
We consider a non-interacting one-dimensional gas accelerated by a constant and uniform external field. The energy absorbed from the field is transferred via elastic collisions to a bath of scattering obstacles. At gas-obstacle encounters…
Thermodynamic principles are often deceptively simple and yet surprisingly powerful. We show how a simple rule, such as the net flow of energy in and out of a moving atom under nonequilibrium steady state condition, can expose the…
This paper presents a continuous, information-theoretic extension of the Free Energy Principle through the concept of Markov blanket density, i.e., a scalar field that quantifies the degree of conditional independence between internal and…
Fluid dynamics accompanies with the entropy production thus increases the local temperature, which plays an important role in charged systems such as the ion channel in biological environment and electrodiffusion in capacitors/batteries. In…
We present a multivariate central limit theorem for a general class of interacting Markov chain Monte Carlo algorithms used to solve nonlinear measure-valued equations. These algorithms generate stochastic processes which belong to the…
A large number of biological systems - from bacteria to sheep - can be described as ensembles of self-propelled agents (active particles) with a complex internal dynamic that controls the agent's behavior: resting, moving slow, moving fast,…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
We continue the investigation of kinetic models of a system in contact via stochastic interactions with several spatially homogeneous thermal reservoirs at different temperatures. Considering models different from those investigated in…
We introduce a finite-time detailed fluctuation theorem for the environmental entropy of the form $\tilde P(\Delta S_{env}) = e^{\Delta S_{env}} \tilde P(-\Delta S_{env})$ for an appropriately weighted probability density of the external…
In this paper we formulate a dynamical fluctuation theory for stationary non equilibrium states (SNS) which covers situations in a nonlinear hydrodynamic regime and is verified explicitly in stochastic models of interacting particles. In…