Entropy production for mechanically or chemically driven biomolecules

DOI10.1007/S10955-006-9148-1zbMATH Open1117.82032arXivcond-mat/0601636OpenAlexW2027142781WikidataQ59459980 ScholiaQ59459980MaRDI QIDQ2641385FDOQ2641385

Authors: Tim Schmiedl, Thomas Speck, Udo Seifert 

Publication date: 20 August 2007

Published in: Journal of Statistical Physics (Search for Journal in Brave)

Abstract: Entropy production along a single stochastic trajectory of a biomolecule is discussed for two different sources of non-equilibrium. For a molecule manipulated mechanically by an AFM or an optical tweezer, entropy production (or annihilation) occurs in the molecular conformation proper or in the surrounding medium. Within a Langevin dynamics, a unique identification of these two contributions is possible. The total entropy change obeys an integral fluctuation theorem and a class of further exact relations, which we prove for arbitrarily coupled slow degrees of freedom including hydrodynamic interactions. These theoretical results can therefore also be applied to driven colloidal systems. For transitions between different internal conformations of a biomolecule involving unbalanced chemical reactions, we provide a thermodynamically consistent formulation and identify again the two sources of entropy production, which obey similar exact relations. We clarify the particular role degenerate states have in such a description.

Full work available at URL: https://arxiv.org/abs/cond-mat/0601636

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zbMATH Keywords

Brownian motionrandom processesthermodynamicsfluctuation phenomenabiomoleculeschemical kinetics in biological systems

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Stochastic methods (Fokker-Planck, Langevin, etc.) applied to problems in time-dependent statistical mechanics (82C31) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45) Irreversible thermodynamics, including Onsager-Machlup theory (82C35)

Cites Work

• A Markov model for kinesin
• Title not available (Why is that?)
• A Gallavotti-Cohen-type symmetry in the large deviation functional for stochastic dynamics
• Fluctuation theorem for stochastic dynamics
• Title not available (Why is that?)
• Brownian motors: noisy transport far from equilibrium
• Microscopic analysis of Clausius-Duhem processes
• Quantal-classical correspondence impulse theory
• Free energy transduction in a chemical motor model

Cited In (13)

• Entropy and Free Energy in Structural Biology
• A model of cooperativity based on restricted binding: kinetic and thermodynamic analysis
• Entropy generation at the cellular level during freezing process of biological materials
• Chemomechanical coupling of molecular motors: thermodynamics, network representations, and balance conditions
• Stochastic thermodynamics: principles and perspectives
• Ergodic pumping: a mechanism to drive biomolecular conformation changes
• Fluctuation relations for non-Markovian and heterogeneous temperature systems
• Entropy production of active particles and for particles in active baths
• Entropy production of a mechanically driven single oligomeric enzyme: a consequence of fluctuation theorem
• Charged Brownian particles: Kramers and Smoluchowski equations and the hydrothermodynamical picture
• On the stochastic thermodynamics of reactive systems
• Fluctuation theorems for stochastic dynamics
• Entropic force between biomembranes

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