Information Thermodynamics On Causal Networks And Its Application To Biochemical Signal Transduction (springer Theses)

In this book the author presents a general formalism of nonequilibrium thermodynamics with complex information flows induced by interactions among multiple fluctuating systems. The author has generalized stochastic thermodynamics with information by using a graphical theory. Characterizing nonequilibrium dynamics by causal networks, he has obtained a novel generalization of the second law of thermodynamics with information that is applicable to quite a broad class of stochastic dynamics such as information transfer between multiple Brownian particles, an autonomous biochemical reaction, and complex dynamics with a time-delayed feedback control. This study can produce further progress in the study of Maxwell’s demon for special cases. As an application to these results, information transmission and thermodynamic dissipation in biochemical signal transduction are discussed. The findings presented here can open up a novel biophysical approach to understanding information processing in living systems. Front Matter....Pages i-xiii Introduction to Information Thermodynamics on Causal Networks....Pages 1-10 Review of Classical Information Theory....Pages 11-23 Stochastic Thermodynamics for Small System....Pages 25-39 Information Thermodynamics Under Feedback Control....Pages 41-50 Bayesian Networks and Causal Networks....Pages 51-60 Information Thermodynamics on Causal Networks....Pages 61-82 Application to Biochemical Signal Transduction....Pages 83-97 Information Thermodynamics as Stochastic Thermodynamics for Small Subsystem....Pages 99-119 Further Applications of Information Thermodynamics on Causal Networks....Pages 121-126 Conclusions....Pages 127-131 Back Matter....Pages 133-133 3.1.1 Detailed Fluctuation Theorem -- 3.1.2 Entropy Production -- 3.1.3 Relative Entropy and the Second Law of Thermodynamics -- 3.1.4 Stochastic Relative Entropy and Integral Fluctuation Theorem -- 3.2 Steady State Thermodynamics and Feedback Cooling -- 3.2.1 Housekeeping Heat and Excess Heat -- 3.2.2 Stochastic Relative Entropy and Hatano--Sasa Identity -- 3.2.3 Stochastic Relative Entropy and Feedback Cooling -- References -- 4 Information Thermodynamics Under Feedback Control -- 4.1 Feedback Control and Entropy Production -- 4.1.1 Stochastic Relative Entropy and Sagawa--Ueda Relation 6.1.2 Examples of Entropy Production on Causal Networks -- 6.1.3 Transfer Entropy on Causal Networks -- 6.1.4 Initial and Final Correlations on Causal Networks -- 6.2 Generalized Second Law on Causal Networks -- 6.2.1 Relative Entropy and Generalized Second Law -- 6.2.2 Examples of Generalized Second Law on Causal Networks -- 6.2.3 Coupled Chemical Reaction Model with Time-Delayed Feedback Loop -- References -- 7 Application to Biochemical Signal Transduction -- 7.1 Biochemical Signal Transduction -- 7.1.1 Sensory Adaptation -- 7.1.2 Mutual Information in Biochemical Signal Transduction 7.2 Information Thermodynamics in Biochemical Signal Transduction -- 7.2.1 Coupled Langevin Model of Sensory Adaptation -- 7.2.2 Information Thermodynamics and Robustness of Adaptation -- 7.2.3 Information Thermodynamics and Conventional Thermordynamics -- 7.2.4 Analytical Calculations -- 7.3 Information Thermodynamics and Noisy-Channel Coding Theorem -- 7.3.1 Analogical Similarity -- 7.3.2 Difference and Biochemical Relevance -- References -- 8 Information Thermodynamics as Stochastic Thermodynamics for Small Subsystem -- 8.1 Information Thermodynamics for Small Subsystem Supervisor's Foreword -- Parts of this thesis have been published in the following journal article: -- Acknowledgments -- Contents -- 1 Introduction to Information Thermodynamics on Causal Networks -- References -- 2 Review of Classical Information Theory -- 2.1 Entropy -- 2.1.1 Shannon Entropy -- 2.1.2 Relative Entropy -- 2.1.3 Mutual Information -- 2.1.4 Transfer Entropy -- 2.2 Noisy-Channel Coding Theorem -- 2.2.1 Communication Channel -- 2.2.2 Noisy-Channel Coding Theorem -- References -- 3 Stochastic Thermodynamics for Small System -- 3.1 Stochastic Thermodynamics 4.1.2 Maxwell's Demon Interpretation of Sagawa--Ueda Relation -- 4.2 Comparison Between Sagawa--Ueda Relation and the Second Law -- 4.2.1 Total Entropy Production and Sagawa--Ueda Relation -- References -- 5 Bayesian Networks and Causal Networks -- 5.1 Bayesian Networks -- 5.1.1 Directed Acyclic Graph -- 5.1.2 Bayesian Networks -- 5.2 Causal Networks -- 5.2.1 Causal Networks -- 5.2.2 Examples of Causal Networks -- References -- 6 Information Thermodynamics on Causal Networks -- 6.1 Entropy on Causal Networks -- 6.1.1 Entropy Production on Causal Networks 8.1.1 Information Thermodynamics for a Multi-dimensional Markov Process