Nonequilibrium thermodynamics and a fluctuation theorem for individual reaction steps in a chemical reaction network
Krishnendu Pal,Biswajit Das,Kinshuk Banerjee,Gautam Gangopadhyay +3 more
- Vol. 638, Iss: 1, pp 012002
TLDR
In this paper, an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the propensities of individual elementary reactions and corresponding reverse reactions is introduced.Abstract:
We have introduced an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the propensities of the individual elementary reactions and the corresponding reverse reactions. The method is a microscopic formulation of the dissipation function in terms of the relative entropy or Kullback-Leibler distance which is based on the analogy of phase space trajectory with the path of elementary reactions in a network of chemical process. We have introduced here a fluctuation theorem valid for each opposite pair of elementary reactions which is useful in determining the contribution of each sub-reaction on the nonequilibrium thermodynamics of overall reaction. The methodology is applied to an oligomeric enzyme kinetics at a chemiostatic condition that leads the reaction to a nonequilibrium steady state for which we have estimated how each step of the reaction is energy driven or entropy driven to contribute to the overall reaction.read more
Citations
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Large deviation theory for the kinetics and energetics of turnover of enzyme catalysis in a chemiostatic flow
Biswajit Das,Gautam Gangopadhyay +1 more
TL;DR: Using some special properties of the Legendre transformation, here, a relation between the fluctuations of fluxes and dissipation rates is provided, and among them, the fluctuation of the turnover rate is routinely estimated but the fluctuations in the dissipation rate is yet to be characterized for small systems.
Journal ArticleDOI
Entropy production for mechanically or chemically driven biomolecules
TL;DR: In this article, entropy change along a single stochastic trajectory of a biomolecule is discussed for two different sources of non-equilibrium entropy, and the total entropy change obeys an integral fluctuation theorem and a class of further exact relations.
References
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Journal ArticleDOI
Exact Stochastic Simulation of Coupled Chemical Reactions
TL;DR: In this article, a simulation algorithm for the stochastic formulation of chemical kinetics is proposed, which uses a rigorously derived Monte Carlo procedure to numerically simulate the time evolution of a given chemical system.
Journal ArticleDOI
A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions
TL;DR: In this paper, an exact method is presented for numerically calculating, within the framework of the stochastic formulation of chemical kinetics, the time evolution of any spatially homogeneous mixture of molecular species which interreact through a specified set of coupled chemical reaction channels.
Book
Handbook of Stochastic Methods: For Physics, Chemistry and the Natural Sciences
TL;DR: The Handbook of Stochastic Methods as mentioned in this paper covers the foundations of Markov systems, stochastic differential equations, Fokker-Planck equations, approximation methods, chemical master equations, and quatum-mechanical Markov processes.
Journal Article
Handbook of stochastic methods for physics, chemistry and the natural sciences, second edition
TL;DR: The Handbook of Stochastic Methods covers systematically and in simple language the foundations of Markov systems, stochastic differential equations, Fokker-Planck equations, approximation methods, chemical master equations, and quatum-mechanical Markov processes.