Entropy production in mesoscopic stochastic thermodynamics: nonequilibrium kinetic cycles driven by chemical potentials, temperatures, and mechanical forces

Nonequilibrium thermodynamics (NET) investigates processes in systems out of global equilibrium. On a mesoscopic level, it provides a statistical dynamic description of various complex phenomena such as chemical reactions, ion transport, diffusion, thermochemical, thermomechanical and mechanochemical fluxes. In the present review, we introduce a mesoscopic stochastic formulation of NET by analyzing entropy production in several simple examples. The fundamental role of nonequilibrium steady-state cycle kinetics is emphasized. The statistical mechanics of Onsager’s reciprocal relations in this context is elucidated. Chemomechanical, thermomechanical, and enzyme-catalyzed thermochemical energy transduction processes are discussed. It is argued that mesoscopic stochastic NET in phase space provides a rigorous mathematical basis of fundamental concepts needed for understanding complex processes in chemistry, physics and biology. This theory is also relevant for nanoscale technological advances.

• Publication year

  2016

• Venue

  Journal of Physics: Condensed Matter

• Publication date

  2016-01-15

• Fields of study

  Medicine, Physics, Chemistry

• Identifiers
  DOI 10.1088/0953-8984/28/15/153004arXiv 1601.04018PMID 26986039
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Motor Proteins and Molecular Motors

  2015cited by this paper
• Far-from-equilibrium kinetic processes

  2015cited by this paper
• Michaelis-Menten kinetics under non-isothermal conditions.

  2015cited by this paper
• Conservation-dissipation formalism of irreversible thermodynamics

  2014cited by this paper
• Thermodynamics of the general diffusion process: Equilibrium supercurrent and nonequilibrium driven circulation with dissipation

  2014cited by this paper
• Ensemble and trajectory thermodynamics: A brief introduction

  2014cited by this paper
• Contact Geometry of Mesoscopic Thermodynamics and Dynamics

  2014cited by this paper
• Mechano-chemical coupling in Belousov-Zhabotinskii reactions.

  2014cited by this paper
• Enzyme Kinetics, Past and Present

  2013cited by this paper
• Coupling between chemical kinetics and mechanics that is both nonlinear and compatible with thermodynamics.

  2013cited by this paper
• Active transport of the Ca2+-pump: introduction of the temperature difference as a driving force

  2013cited by this paper
• Stochastic thermodynamics, fluctuation theorems and molecular machines

  2012cited by this paper
• Fluctuations in extended mass-action-law dynamics

  2012cited by this paper
• Kinetic and mesoscopic non-equilibrium description of the Ca2+ pump: a comparison

  2012cited by this paper
• Dissipation, generalized free energy, and a self-consistent nonequilibrium thermodynamics of chemically driven open subsystems.

  2011cited by this paper
• Equalities and Inequalities: Irreversibility and the Second Law of Thermodynamics at the Nanoscale

  2011cited by this paper
• Stochastic thermodynamics under coarse graining.

  2011cited by this paper
• Entropy demystified the "thermo"-dynamics of stochastically fluctuating systems.

  2009cited by this paper
• Three detailed fluctuation theorems.

  2009cited by this paper
• Physical origins of entropy production, free energy dissipation, and their mathematical representations.

  2009cited by this paper
• The measurable heat flux that accompanies active transport by Ca2+-ATPase.

  2008cited by this paper
• Cooperativity and specificity in enzyme kinetics: a single-molecule time-based perspective.

  2008cited by this paper
• Thermoelectric efficiency at maximum power in a quantum dot

  2008cited by this paper
• Phosphorylation energy hypothesis: open chemical systems and their biological functions.

  2007cited by this paper
• Reducing intrinsic biochemical noise in cells and its thermodynamic limit.

  2006cited by this paper
• Open-system nonequilibrium steady state: statistical thermodynamics, fluctuations, and chemical oscillations.

  2006cited by this paper
• Hydrodynamic Fluctuations in Fluids and Fluid Mixtures

  2006cited by this paper
• Generalized Haldane equation and fluctuation theorem in the steady-state cycle kinetics of single enzymes.

  2005cited by this paper
• A highway in state space for reactors with minimum entropy production

  2005cited by this paper
• Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium.

  2005cited by this paper
• Motor protein with nonequilibrium potential: Its thermodynamics and efficiency.

  2004cited by this paper
• Mathematical Theory of Nonequilibrium Steady States

  2004cited by this paper
• Nonequilibrium thermodynamics

  2003cited by this paper
• Mesoscopic Nonequilibrium Thermodynamics Gives the Same Thermodynamic Basis to Butler-Volmer and Nernst Equations

  2003cited by this paper
• Notes on Landauer's Principle, Reversible Computation, and Maxwell's Demon

  2002cited by this paper
• Thermodynamics of the General Diffusion Process: Time-Reversibility and Entropy Production

  2002cited by this paper
• Thermodynamics of Small Systems

  2002cited by this paper
• Kinetic Timing: A Novel Mechanism That Improves the Accuracy of GTPase Timers in Endosome Fusion and Other Biological Processes

  2002cited by this paper
• Mesoscopic nonequilibrium thermodynamics of single macromolecules and dynamic entropy-energy compensation.

  2001cited by this paper
• Book Review: An Introduction to Chaos in Nonequilibrium Statistical Mechanics Cambridge. J. R. Dorfman, Cambridge Lecture Notes in Physics 14, Cambridge University 1999

  2001cited by this paper
• The mathematical theory of molecular motor movement and chemomechanical energy transduction

  2000cited by this paper
• Equations for stochastic macromolecular mechanics of single proteins: Equilibrium fluctuations, transient kinetics, and nonequilibrium steady-state

  2000cited by this paper
• A simple theory of motor protein kinetics and energetics. II.

  2000cited by this paper
• The force exerted by a molecular motor.

  1999cited by this paper
• Molecular motors and the forces they exert

  1999cited by this paper
• An Introduction to Chaos in Nonequilibrium Statistical Mechanics: Gibbs' picture: mixing systems

  1999influential reference
• Entropy-enthalpy compensation : Conformational fluctuation and induced-fit

  1998cited by this paper
• Statistical Physics: An Advanced Approach with Applications

  1998cited by this paper
• Energy transduction in the F1 motor of ATP synthase

  1998cited by this paper
• Chaos, Scattering and Statistical Mechanics

  1998cited by this paper
• A simple theory of motor protein kinetics and energetics.

  1997cited by this paper
• Entropy‐enthalpy compensation: Perturbation and relaxation in thermodynamic systems

  1996cited by this paper
• Stochastic Processes in Physics and Chemistry

  1995cited by this paper
• The dynamic origin of increasing entropy

  1989cited by this paper
• The Theory of Polymer Dynamics

  1986cited by this paper
• Derivation of the relation between the linear Onsager coefficients and the equilibrium one-way cycle fluxes of a biochemical kinetic diagram.

  1983cited by this paper
• The linear Onsager coefficients for biochemical kinetic diagrams as equilibrium one-way cycle fluxes

  1982cited by this paper
• Microfilament or microtubule assembly or disassembly against a force.

  1981cited by this paper
• Stochastic processes in physics and chemistry

  1981cited by this paper
• Free Energy Transduction in Biology: The Steady-State Kinetic and Thermodynamic Formalism

  1977cited by this paper
• Network theory of microscopic and macroscopic behavior of master equation systems

  1976cited by this paper
• Kinetic amplification of enzyme discrimination.

  1975cited by this paper
• Stochastics of cycle completions (fluxes) in biochemical kinetic diagrams.

  1975cited by this paper
• Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems

  1975cited by this paper
• Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity.

  1974cited by this paper
• The Relationship between Stochastic and Deterministic Models for Chemical Reactions

  1972cited by this paper
• Coupling of Phosphorylation to Electron and Hydrogen Transfer by a Chemi-Osmotic type of Mechanism

  1961cited by this paper
• Irreversible gibbsian ensembles

  1957cited by this paper
• New Approach to Nonequilibrium Processes

  1955cited by this paper
• Fluctuations and Irreversible Processes

  1953cited by this paper
• Fluctuations and Irreversible Process. II. Systems with Kinetic Energy

  1953cited by this paper
• Brownian Motion in the Theory of Irreversible Processes

  1952cited by this paper
• The Statistical Method of Gibbs in Irreversible Change

  1950cited by this paper
• Etude thermodynamique des phénomènes irréversibles

  1947cited by this paper
• On Onsager's Principle of Microscopic Reversibility

  1945cited by this paper
• Zur Thermodynamik der Thermodiffusion

  1941cited by this paper
• Brownian motion in a field of force and the diffusion model of chemical reactions

  1940cited by this paper
• Reciprocal Relations in Irreversible Processes. II.

  1931cited by this paper
• A New Principle of Equilibrium.

  1925cited by this paper
• XXXI. The Bakerian lecture.-On the electro-dynamic qualities of metals

  year unknowncited by this paper

• Optimum entropy generation structure and partial efficiencies of finite-time carnot heat engines under performance limit conditions

  2026cites this paper
• Effect of Temperature in Dynamic Catalysis

  2025cites this paper
• Identifying nonequilibrium degrees of freedom in high-dimensional stochastic systems

  2025cites this paper
• Energy dissipation in ensembles of catalytic Janus particles.

  2025cites this paper
• Geometric theory of (extended) time-reversal symmetries in stochastic processes: II. Field theory

  2025cites this paper
• Coarse-Graining Chemical Networks by Trimming to Preserve Energy Dissipation.

  2025cites this paper
• Deriving the Forces of Nonequilibria from Two Laws

  2024cites this paper
• Mesoscopic and Macroscopic Entropy Balance Equations in a Stochastic Dynamics and Its Deterministic Limit

  2024cites this paper
• Theoretical Understanding of Dynamic Catalysis

  2024cites this paper
• Dynamics of systems with varying number of particles: from Liouville equations to general master equations for open systems

  2024cites this paper
• Synergy among Pausing, Intrinsic Proofreading, and Accessory Proteins Results in Optimal Transcription Speed and Tolerable Accuracy.

  2023cites this paper
• Fluctuation Theorem on a Riemannian Manifold

  2023cites this paper
• Analytical Decomposition of Transition Flux to Cycle Durations via Integration of Transition Times

  2022cites this paper
• Programmable and Chemically Fueled DNA Coacervates by Transient Liquid-Liquid Phase Separation

  2022cites this paper
• Some Recent Advances in Energetic Variational Approaches

  2022cites this paper
• Nonequilibrium Thermodynamics in Biochemical Systems and Its Application

  2021cites this paper
• Recent Advances in Conservation–Dissipation Formalism for Irreversible Processes

  2021cites this paper
• Cycle Flux Ranking of Network Analysis in Quantum Thermal Devices.

  2021cites this paper
• Generalized energy-conserving dissipative particle dynamics revisited: Insight from the thermodynamics of the mesoparticle leading to an alternative heat flow model.

  2021cites this paper
• Entropy production in random billiards

  2021cites this paper
• Nonequilibrium model of short-range repression in gene transcription regulation.

  2020influential citation
• Advanced Tailored Randomness: A Novel Approach for Improving the Efficacy of Biological Systems

  2020cites this paper
• Field theory of reaction-diffusion: Law of mass action with an energetic variational approach.

  2020cites this paper
• The statistical foundation of entropy in extended irreversible thermodynamics

  2020cites this paper
• Bivectorial Mesoscopic Nonequilibrium Thermodynamics: Landauer-Bennett-Hill Principle, Cycle Affinity and Vorticity Potential

  2020cites this paper
• Energetic and entropic cost due to overlapping of Turing-Hopf instabilities in the presence of cross diffusion.

  2020cites this paper
• ATP-powered molecular recognition to engineer transient multivalency and self-sorting 4D hierarchical systems

  2020cites this paper
• Do We Understand the Mechanisms used by Biological Systems to Correct their Errors?

  2020cites this paper
• Grand canonical description of equilibrium and non-equilibrium systems using spin formalism

  2020cites this paper
• Programmable and Chemically Fueled DNA Coacervates by Transient Liquid-Liquid Phase Separation.

  2020cites this paper
• Improved bounds on entropy production in living systems

  2020cites this paper
• Bivectorial Nonequilibrium Thermodynamics: Cycle Affinity, Vorticity Potential, and Onsager’s Principle

  2020cites this paper
• Entropy Production in Random Billiards and the Second Law of Thermodynamics

  2019cites this paper
• Stochastic dynamics: Models for intrinsic and extrinsic noises and their applications

  2019cites this paper
• Representations and divergences in the space of probability measures and stochastic thermodynamics

  2019cites this paper
• The Dynamics of Biological Systems

  2019cites this paper
• Ternary Representation of Stochastic Change and the Origin of Entropy and Its Fluctuations

  2019cites this paper
• Stochastic Population Kinetics and Its Underlying Mathematicothermodynamics

  2019cites this paper
• Theory of Nonequilibrium Free Energy Transduction by Molecular Machines.

  2019cites this paper
• Stochastic thermodynamics and modes of operation of a ribosome: A network theoretic perspective.

  2019cites this paper
• Trade-Offs between Error, Speed, Noise, and Energy Dissipation in Biological Processes with Proofreading.

  2019cites this paper
• Entropy productions in dissipative systems

  2019cites this paper
• Quantifying dissipation using fluctuating currents

  2018cites this paper
• Dissipation at the angstrom scale: Probing the surface and interior of an enzyme.

  2018cites this paper
• Stochastic thermodynamics and entropy production of chemical reaction systems.

  2018cites this paper
• Entropy Productions and Their Mathematical Representations: Clausius' vs. Kelvin's Views of the Second Law and Irreversibility

  2018cites this paper
• Some Problems in Stochastic Dynamics and Statistical Analysis of Single-Cell Biology of Cancer

  2018cites this paper
• Finite-time fluctuation theorem for diffusion-influenced surface reactions

  2018cites this paper
• Mathematical Representation of Clausius’ and Kelvin’s Statements of the Second Law and Irreversibility

  2018cites this paper
• Information and entropic force: physical description of biological cells, chemical reaction kinetics, and information theory

  2017cites this paper
• Allocating dissipation across a molecular machine cycle to maximize flux

  2017cites this paper
• Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics: differentiation in living matters

  2017cites this paper
• Mesoscopic kinetic basis of macroscopic chemical thermodynamics: A mathematical theory.

  2016cites this paper
• Stochastic dynamics: Markov chains and random transformations

  2016cites this paper
• Potential of Entropic Force in Markov Systems with Nonequilibrium Steady State, Generalized Gibbs Function and Criticality

  2016cites this paper
• Infimum Law and First-Passage-Time Fluctuation Theorem for Entropy Production

  2016cites this paper
• Nonlinear Stochastic Dynamics of Complex Systems, III: Nonequilibrium Thermodynamics of Self-Replication Kinetics

  2016cites this paper
• Mathematical Formalism of Nonequilibrium Thermodynamics for Nonlinear Chemical Reaction Systems with General Rate Law

  2016cites this paper
• Chemical reaction kinetic perspective with mesoscopic nonequilibrium thermodynamics

  2016cites this paper
• Statistics of Infima and Stopping Times of Entropy Production and Applications to Active Molecular Processes

  2016cites this paper
• Nonequilibrium thermodynamic formalism of nonlinear chemical reaction systems with Waage–Guldberg’s law of mass action

  2016cites this paper
• PUBLICATIONS and PRESENTATIONS

  2016cites this paper
• Mathematical Formalism of Nonequilibrium Thermodynamics for Nonlinear Chemical Reaction Systems with General Rate Law

  2016cites this paper
• Nonequilibrium steady state of biochemical cycle kinetics under non-isothermal conditions

  2016cites this paper