10 citations · 21 across the 15 of their papers we have counts for
15 papers
Convex Analysis of Relaxation Dynamics in Chemical Reaction Networks and Generalized Gradient Flows
Keisuke Sugie, Dimitri Loutchko, Tetsuya J. Kobayashi
We obtain bounds on the Kullback--Leibler divergence to equilibrium for mass-action chemical reaction networks (CRNs) with equilibrium. The associated decay rates are characterized…
Information geometry of perturbed gradient flow systems on hypergraphs: A perspective towards nonequilibrium physics
Dimitri Loutchko, Keisuke Sugie, Tetsuya J Kobayashi
This article serves to concisely review the link between gradient flow systems on hypergraphs and information geometry which has been established within the last five years. Gradie…
Information geometry of chemical reaction networks: Cramer-Rao bound and absolute sensitivity revisited
Dimitri Loutchko, Yuki Sughiyama, Tetsuya J. Kobayashi
Information geometry is based on classical Legendre duality but allows to incorporate additional structure such as algebraic constraints and Bregman divergence functions. It is nat…
Transitions and Thermodynamics on Species Graphs of Chemical Reaction Networks
Keisuke Sugie, Dimitri Loutchko, Tetsuya J. Kobayashi
Chemical reaction networks (CRNs) exhibit complex dynamics governed by their underlying network structure. In this paper, we propose a novel approach to study the dynamics of CRNs…
Cramer-Rao bound and absolute sensitivity in chemical reaction networks
Dimitri Loutchko, Yuki Sughiyama, Tetsuya J. Kobayashi
Chemical reaction networks (CRN) comprise an important class of models to understand biological functions such as cellular information processing, the robustness and control of met…
The Geometry of Thermodynamic Uncertainty Relations in Chemical Reaction Networks
Dimitri Loutchko, Yuki Sughiyama, Tetsuya J. Kobayashi
Recently, Hessian geometry - an extension of information geometry - has emerged as a framework to naturally connect the geometries appearing in the theory of chemical reaction netw…
Information Geometry of Dynamics on Graphs and Hypergraphs
Tetsuya J. Kobayashi, Dimitri Loutchko, Atsushi Kamimura +2
We introduce a new information-geometric structure associated with the dynamics on discrete objects such as graphs and hypergraphs. The presented setup consists of two dually flat…
An algebraic characterization of self-generating chemical reaction networks using semigroup models
Dimitri Loutchko
The ability of a chemical reaction network to generate itself by catalyzed reactions from constantly present environmental food sources is considered a fundamental property in orig…
Geometry of Nonequilibrium Chemical Reaction Networks and Generalized Entropy Production Decompositions
Tetsuya J. Kobayashi, Dimitri Loutchko, Atsushi Kamimura +1
We derive the Hessian geometric structure of nonequilibrium chemical reaction networks (CRN) on the flux and force spaces induced by the Legendre duality of convex dissipation func…
Riemannian Geometry of Optimal Driving and Thermodynamic Length and its Application to Chemical Reaction Networks
Dimitri Loutchko, Yuki Sughiyama, Tetsuya J. Kobayashi
It is known that the trajectory of an endoreversibly driven system with minimal dissipation is a geodesic on the equilibrium state space. Thereby, the state space is equipped with…
Chemical Thermodynamics for Growing Systems
Yuki Sughiyama, Atsushi Kamimura, Dimitri Loutchko +1
We consider growing open chemical reaction systems (CRSs), in which autocatalytic chemical reactions are encapsulated in a finite volume and its size can change in conjunction with…
Kinetic Derivation of the Hessian Geometric Structure in Chemical Reaction Systems
Tetsuya J. Kobayashi, Dimitri Loutchko, Atsushi Kamimura +1
The theory of chemical kinetics form the basis to describe the dynamics of chemical systems. Owing to physical and thermodynamic constraints, chemical reaction systems possess vari…
A Hessian Geometric Structure of Chemical Thermodynamic Systems with Stoichiometric Constraints
Yuki Sughiyama, Dimitri Loutchko, Atsushi Kamimura +1
We establish a Hessian geometric structure in chemical thermodynamics which describes chemical reaction networks (CRNs) with equilibrium states. In our setup, the ideal gas assumpt…
Algebraic Coarse-Graining of Biochemical Reaction Networks
Dimitri Loutchko
Biological systems exhibit processes on a wide range of time and length scales. This work demonstrates that models, wherein the interaction between system constituents is captured…
Semigroup models for biochemical reaction networks
Dimitri Loutchko
The catalytic reaction system (CRS) formalism by Hordijk and Steel is a versatile method to model autocatalytic biochemical reaction networks. It is particularly suited, and has be…