Hessian geometry of nonequilibrium chemical reaction networks and entropy production decompositions
Reads0
Chats0
TLDR
In this article , the authors derive the Hessian geometric structure of nonequilibrium chemical reaction networks on the flux and force spaces induced by the Legendre duality of convex dissipation functions and characterize their dynamics as a generalized flow.Abstract:
We derive the Hessian geometric structure of nonequilibrium chemical reaction networks on the flux and force spaces induced by the Legendre duality of convex dissipation functions and characterize their dynamics as a generalized flow. With this geometric structure, we can extend theories of nonequilibrium systems with quadratic dissipation functions to more general cases with nonquadratic ones, which are pivotal for studying chemical reaction networks. By applying generalized notions of orthogonality in Hessian geometry to chemical reaction networks, two generalized decompositions of the entropy production rate are obtained, each of which captures gradient-flow and minimum-dissipation aspects in nonequilibrium dynamics. read more
Citations
More filters
Journal ArticleDOI
Geometric thermodynamics for the Fokker–Planck equation: stochastic thermodynamic links between information geometry and optimal transport
TL;DR: In this paper , a geometric framework of non-equilibrium thermodynamics in terms of information geometry and optimal transport theory has been proposed, which is useful for obtaining thermodynamic trade-off relations between the thermodynamic cost and the fluctuation of the observable, optimal protocols for the minimum cost.
Journal ArticleDOI
Information geometry of excess and housekeeping entropy production
TL;DR: In this article , the authors show that entropy production (EP) has an information-geometric structure, which allows them to decompose EP into nonnegative contributions from different types of forces.
Journal ArticleDOI
Riemannian geometry of optimal driving and thermodynamic length and its application to chemical reaction networks
TL;DR: In this article , a weighted Fisher information metric on the space of chemical concentrations is introduced to characterize the dissipation caused by diffusive driving, with arbitrary dissipation rate constants.
Complete characterization of robust perfect adaptation in biochemical reaction networks
TL;DR: In this article , an approach for finding all RPA properties that are realized for a generic choice of kinetics for general deterministic chemical reaction systems is presented, which is accomplished by proving that an RPA property is represented by a subnetwork with certain topological features.
Journal ArticleDOI
Cellular gradient flow structure linking single-cell-level rules and population-level dynamics
TL;DR: In this paper , the authors reveal that these two levels are naturally connected via a gradient flow structure of heterogeneous cellular populations and that biologically prevalent single-cell rules, such as unidirectional type switching and hierarchical order in types, emerge from this structure.
References
More filters
Journal ArticleDOI
Reciprocal Relations in Irreversible Processes. II.
TL;DR: In this article, a general reciprocal relation applicable to transport processes such as the conduction of heat and electricity, and diffusion, is derived from the assumption of microscopic reversibility, and certain average products of fluctuations are considered.
Journal ArticleDOI
On the Equilibrium of Heterogeneous Substances
TL;DR: The article ''On the Equilibrium of Heterogeneous Substances'', which was published in ''Transactions of the Connecticut Academy of Arts and Sciences'', vol. 3 (1874-78), pp. 108-248 and 343-524 as mentioned in this paper
Journal ArticleDOI
A computational fluid mechanics solution to the Monge-Kantorovich mass transfer problem
Jean-David Benamou,Yann Brenier +1 more
TL;DR: The Monge-Kantorovich mass transfer problem is reset in a fluid mechanics framework and numerically solved by an augmented Lagrangian method.
Journal ArticleDOI
Fluctuations and Irreversible Processes
Lars Onsager,S. Machlup +1 more
TL;DR: In this paper, the probability of a given succession of (nonequilibrium) states of a spontaneously fluctuating thermodynamic system is calculated, on the assumption that the macroscopic variables defining a state are Gaussian random variables whose average behavior is given by the laws governing irreversible processes.
Journal ArticleDOI
Network theory of microscopic and macroscopic behavior of master equation systems
TL;DR: In this paper, a general microscopic and macroscopic theory is developed for systems which are governed by a (linear) master equation, and the results are obtained mostly by application of some basic theorems of mathematical graph theory.