Entropy production for mechanically or chemically driven biomolecules
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Publication:2641385
Brownian motionrandom processesthermodynamicsfluctuation phenomenabiomoleculeschemical kinetics in biological systems
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)
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.
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Cited in
(13)- Fluctuation theorems for stochastic dynamics
- 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
- Stochastic thermodynamics: principles and perspectives
- Chemomechanical coupling of molecular motors: thermodynamics, network representations, and balance conditions
- 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
- Entropic force between biomembranes
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