44 citations · 121 across the 21 of their papers we have counts for
21 papers
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…
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…
Cellular gradient flow structure connects single-cell-level rules and population-level dynamics
Shuhei A. Horiguchi, Tetsuya J. Kobayashi
In multicellular systems, the single-cell behaviors should be coordinated consistently with the overall population dynamics and functions. However, the interrelation between single…
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…
Optimal sensing and control of run-and-tumble chemotaxis
Kento Nakamura, Tetsuya J. Kobayashi
Run-and-tumble chemotaxis is one of the representative search strategies of an odor source via sensing its spatial gradient. The optimal ways of sensing and control in the run-and-…
Acceleration of Evolutionary Processes by Learning and Extended Fisher's Fundamental Theorem
So Nakashima, Tetsuya J. Kobayashi
Natural selection is general and powerful concept not only to explain evolutionary processes of biological organisms but also to design engineering systems such as genetic algorith…
Forward and Backward Bellman equations improve the efficiency of EM algorithm for DEC-POMDP
Takehiro Tottori, Tetsuya J. Kobayashi
Decentralized partially observable Markov decision process (DEC-POMDP) models sequential decision making problems by a team of agents. Since the planning of DEC-POMDP can be interp…
Understanding how T helper cells learn to coordinate effective immune responses through the lens of reinforcement learning
Takuya Kato, Tetsuya J. Kobayashi
The adaptive immune system of vertebrates can detect, respond to, and memorize diverse pathogens from past experience. While the clonal selection of T helper (Th) cells is the simp…
Lineage EM Algorithm for Inferring Latent States from Cellular Lineage Trees
So Nakashima, Yuki Sughiyama, Tetsuya J. Kobayashi
Phenotypic variability in a population of cells can work as the bet-hedging of the cells under an unpredictably changing environment, the typical example of which is the bacterial…
Fitness response relation of a multi-type age-structured population dynamics
Yuki Sughiyama, So Nakashima, Tetsuya J. Kobayashi
We construct a pathwise formulation for a multi-type age-structured population dynamics, which involves an age-dependent cell replication and transition of gene- or phenotypes. By…
Individual Sensing can Gain more Fitness than its Information
Tetsuya J. Kobayashi, Yuki Sughiyama
Mutual information and its causal variant, directed information, have been widely used to quantitatively characterize the performance of biological sensing and information transduc…
Stochastic and Information-thermodynamic Structures of Population Dynamics in Fluctuating Environment
Tetsuya J. Kobayashi, Yuki Sughiyama
Adaptation in a fluctuating environment is a process of fueling environmental information to gain fitness. Living systems have gradually developed strategies for adaptation from ra…
Balancing specificity, sensitivity and speed of ligand discrimination by zero-order ultraspecificity
Masashi K. Kajita, Kazuyuki Aihara, Tetsuya J. Kobayashi
Specific interactions between receptors and their target ligands in the presence of non-target ligands are crucial for biological processes such as T cell ligand discrimination. To…
Discreteness-induced transitions in multi-body reaction systems
Yohei Saito, Yuki Sughiyama, Kunihiko Kaneko +1
A decrease in system size can induce qualitatively different behavior compared to the macroscopic behavior of the corresponding large-size system. The mechanisms of this transition…
Steady state thermodynamics in population dynamics
Yuki Sughiyama, Tetsuya J. Kobayashi
We report that population dynamics in fluctuating environment accompanies mathematically equivalent structure to steady state thermodynamics. By employing the structure, population…
Fluctuation Relations of Fitness and Information in Population Dynamics
Tetsuya J. Kobayashi, Yuki Sughiyama
Phenotype-switching with and without sensing environment is a ubiquitous strategy of organisms to survive in fluctuating environment. Fitness of a population of organisms with phen…
Feedback Regulation and its Efficiency in Biochemical Networks
Tetsuya J. Kobayashi, Ryo Yokota, Kazuyuki Aihara
Intracellular biochemical networks fluctuate dynamically due to various internal and external sources of fluctuation. Dissecting the fluctuation into biologically relevant componen…