arXiv subjects

Sosuke Ito

Publications and source records attributed to Sosuke Ito.

At least 37 records · Page 2Linked to original sources

arXiv2024

Geometric thermodynamics of reaction-diffusion systems: Thermodynamic trade-off relations and optimal transport for pattern formation

We establish universal relations between pattern formation and dissipation with a geometric approach to nonequilibrium thermodynamics of deterministic reaction-diffusion systems. We first provide a way to systematically decompose the entropy production rate (EPR) based on the orthogonality of thermodynamic forces, in this way identifying the amount of dissipation caused by each factor. This enables us to extract the excess EPR that genuinely contributes to the time evolution of patterns. We also show that a similar geometric method further decomposes the EPR into detailed contributions, e.g., the dissipation from each point in real or wavenumber space. Second, we relate the excess EPR to the details of the change in patterns through two types of thermodynamic trade-off relations for reaction-diffusion systems: thermodynamic speed limits and thermodynamic uncertainty relations. The former relates dissipation and the speed of pattern formation, and the latter bounds the excess EPR with partial information on patterns, such as specific Fourier components of concentration distributions. In connection with the derivation of the thermodynamic speed limits, we also extend optimal transport theory to reaction-diffusion systems, which enables us to measure the speed of the time evolution. This extension of optimal transport also solves the minimization problem of the dissipation associated with the transition between two patterns, and it constructs energetically efficient protocols for pattern formation. We numerically demonstrate our results using chemical traveling waves in the Fisher-Kolmogorov-Petrovsky-Piskunov equation and changes in symmetry in the Brusselator model. Our results apply to general reaction-diffusion systems and contribute to understanding the relations between pattern formation and unavoidable dissipation.

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arXiv2024

Microscopic theory of Mpemba effects and a no-Mpemba theorem for monotone many-body systems

Mpemba effects (MPEs), where a hotter system cools faster than a colder one, present intriguing anomalies in relaxation processes. Despite their universal observation and significant fundamental and practical implications, a comprehensive theoretical understanding based on microscopic properties remains elusive. In this Letter, we introduce two universal frameworks for classical systems to address this gap. Firstly, we reveal that MPEs, traditionally defined by macroscopic temperature comparisons, can be understood through microstate comparisons. This insight offers a straightforward and universal microscopic perspective on MPEs, relevant for experiments and numerical simulations to identify their microscopic origins. Secondly, we establish a "no-Mpemba theorem," a rigorous sufficient condition for the absence of MPEs, thereby identifying specific classes of systems devoid of these effects. Our findings are exemplified using ferromagnetic Ising models and one-dimensional multiparticle systems, demonstrating the practical applicability of our theoretical advancements.

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arXiv2024

Decomposing Thermodynamic Dissipation of Linear Langevin Systems via Oscillatory Modes and Its Application to Neural Dynamics

Recent developments in stochastic thermodynamics have elucidated various relations between the entropy production rate (thermodynamic dissipation) and the physical limits of information processing in nonequilibrium dynamical systems. These findings have opened new perspectives in analyzing real biological systems. In neuroscience, the importance of quantifying entropy production has attracted attention for understanding information processing in the brain. However, the relationship between the entropy production rate and oscillations, which are common in many biological systems, remains unclear. For instance, neural oscillations like delta, theta, and alpha waves play crucial roles in brain information processing. Here, we derive a novel decomposition of the entropy production rate of linear Langevin systems. We show that one component of the entropy production rate, called the housekeeping entropy production rate, can be decomposed into independent positive contributions from oscillatory modes. Our decomposition enables us to calculate the contribution of oscillatory modes to the housekeeping entropy production rate. In addition, when the noise matrix is diagonal, the contribution of each oscillatory mode can be further decomposed into the contribution of each system element. To demonstrate the utility of our decomposition, we applied it to an electrocorticography (ECoG) dataset recorded during awake and anesthetized conditions in monkeys, where the oscillatory properties change drastically. We showed consistent trends across different monkeys: the contribution of delta band was larger in the anesthetized condition than in the awake condition, while those from higher frequency bands, such as the theta band, were smaller. These results allow us to interpret the changes in neural oscillation in terms of stochastic thermodynamics and the physical limits of information processing.

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arXiv2024

Two applications of stochastic thermodynamics to hydrodynamics

Recently, the theoretical framework of stochastic thermodynamics has been revealed to be useful for macroscopic systems. However, despite its conceptual and practical importance, the connection to hydrodynamics has yet to be explored. In this Letter, we reformulate the thermodynamics of compressible and incompressible Newtonian fluids so that it becomes comparable to stochastic thermodynamics and unveil their connections; we obtain the housekeeping--excess decomposition of entropy production rate (EPR) for hydrodynamic systems and find a lower bound on EPR given by relative fluctuation similar to the thermodynamic uncertainty relation. These results not only prove the universality of stochastic thermodynamics but also suggest the potential extensibility of the thermodynamic theory of hydrodynamic systems.

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arXiv2024

Inferring nonequilibrium thermodynamics from tilted equilibrium using information-geometric Legendre transform

Nonstationary thermodynamic quantities depend on the full details of nonstationary probability distributions, making them difficult to measure directly in experiments and numerics. We propose a method to infer thermodynamic quantities in relaxation processes by measuring only a few observables, using additional information obtained from measurements in tilted equilibrium, i.e., equilibrium with external fields applied. Our method is applicable to arbitrary classical stochastic systems, possibly underdamped, that relax to equilibrium. The method allows us to compute the exact value of the minimum entropy production (EP) compatible with the nonstationary observations, giving a tight lower bound on the true EP. Under a certain additional condition, it also allows the inference of the EP rate, thermodynamic forces, and a constraint on relaxation paths. Our method uses a Legendre transform of EP at the level of probability distributions, which we develop based on a similar Legendre transform in information geometry.

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arXiv2024

Thermodynamic bounds on spectral perturbations, with applications to oscillations and relaxation dynamics

In discrete-state Markovian systems, many important properties of correlations functions and relaxation dynamics depend on the spectrum of the rate matrix. Here we demonstrate the existence of a universal trade-off between thermodynamic and spectral properties. We show that the entropy production rate, the fundamental thermodynamic cost of a nonequilibrium steady state, bounds the difference between the eigenvalues of a nonequilibrium rate matrix and a reference equilibrium rate matrix. Using this result, we derive thermodynamic bounds on the spectral gap, which governs autocorrelations times and the speed of relaxation to steady state. We also derive thermodynamic bounds on the imaginary eigenvalues, which govern the speed of oscillations. We illustrate our approach using a simple model of biomolecular sensing.

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arXiv2023

Geometric thermodynamics for the Fokker-Planck equation: Stochastic thermodynamic links between information geometry and optimal transport

We propose a geometric theory of non-equilibrium thermodynamics, namely geometric thermodynamics, using our recent developments of differential-geometric aspects of entropy production rate in non-equilibrium thermodynamics. By revisiting our recent results on geometrical aspects of entropy production rate in stochastic thermodynamics for the Fokker-Planck equation, we introduce a geometric framework of non-equilibrium thermodynamics in terms of information geometry and optimal transport theory. We show that the proposed geometric framework is useful for obtaining several non-equilibrium thermodynamic relations, such as thermodynamic trade-off relations between the thermodynamic cost and the fluctuation of the observable, optimal protocols for the minimum thermodynamic cost and the decomposition of the entropy production rate for the non-equilibrium system. We clarify several stochastic-thermodynamic links between information geometry and optimal transport theory via the excess entropy production rate based on a relation between the gradient flow expression and information geometry in the space of probability densities and a relation between the velocity field in optimal transport and information geometry in the space of path probability densities.

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arXiv2023

Game-theoretical approach to minimum entropy productions in information thermodynamics

In a situation where each player has control over the transition probabilities of each subsystem, we game-theoretically analyze the optimization problem of minimizing both the partial entropy production of each subsystem and a penalty for failing to achieve a given state transition. In the regime of linear irreversible thermodynamics, we obtain the Nash equilibrium solution of the probability flow and calculate each partial entropy production for this solution. We find a trade-off such that a partial entropy production should be larger if we want the other partial entropy production to be smaller. The total entropy production can be minimized if each subsystem equally shares the penalty. We identify that this trade-off is due to the interacting contribution of the probability flow and discuss a possible biological validity for Escherichia coli chemotaxis.

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arXiv2023

Thermodynamic Bound on the Asymmetry of Cross-Correlations

The principle of microscopic reversibility says that, in equilibrium, two-time cross-correlations are symmetric under the exchange of observables. Thus, the asymmetry of cross-correlations is a fundamental, measurable, and often-used statistical signature of deviation from equilibrium. Here we find a simple and universal inequality that bounds the magnitude of asymmetry by the cycle affinity, i.e., the strength of thermodynamic driving. Our result applies to a large class of systems and all state observables, and it suggests a fundamental thermodynamic cost for various nonequilibrium functions quantified by the asymmetry. It also provides a powerful tool to infer affinity from measured cross-correlations, in a different and complementary way to the thermodynamic uncertainty relations. As an application, we prove a thermodynamic bound on the coherence of noisy oscillations, which was previously conjectured by Barato and Seifert [Phys. Rev. E 95, 062409 (2017)]. We also derive a thermodynamic bound on directed information flow in a biochemical signal transduction model.

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arXiv2023

Housekeeping and excess entropy production for general nonlinear dynamics

We propose a housekeeping/excess decomposition of entropy production for general nonlinear dynamics in a discrete space, including chemical reaction networks and discrete stochastic systems. We exploit the geometric structure of thermodynamic forces to define the decomposition; this does not rely on the notion of a steady state, and even applies to systems that exhibit multistability, limit cycles, and chaos. In the decomposition, distinct aspects of the dynamics contribute separately to entropy production: the housekeeping part stems from a cyclic mode that arises from external driving, generalizing Schnakenberg's cyclic decomposition to non-steady states, while the excess part stems from an instantaneous relaxation mode that arises from conservative forces. Our decomposition refines previously known thermodynamic uncertainty relations and speed limits. In particular, it not only improves an optimal-transport-theoretic speed limit, but also extends the optimal transport theory of discrete systems to nonlinear and nonconservative settings.

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arXiv2023

A geometric speed limit for acceleration by natural selection in evolutionary processes

We derived a new speed limit in population dynamics, which is a fundamental limit on the evolutionary rate. By splitting the contributions of selection and mutation to the evolutionary rate, we obtained the new bound on the speed of arbitrary observables, named the selection bound, that can be tighter than the conventional Cramér--Rao bound. Remarkably, the selection bound can be much tighter if the contribution of selection is more dominant than that of mutation. This tightness can be geometrically characterized by the correlation between the observable of interest and the growth rate. We also numerically illustrate the effectiveness of the selection bound in the transient dynamics of evolutionary processes and discuss how to test our speed limit experimentally.

q-bio.PE↗

arXiv2022

Information geometry of excess and housekeeping entropy production

A nonequilibrium system is characterized by a set of thermodynamic forces and fluxes which give rise to entropy production (EP). We show that these forces and fluxes have an information-geometric structure, which allows us to decompose EP into contributions from different types of forces in general (linear and nonlinear) discrete systems. We focus on the excess and housekeeping decomposition, which separates contributions from conservative and nonconservative forces. Unlike the Hatano-Sasa decomposition, our housekeeping/excess terms are always well-defined, including in systems with odd variables and nonlinear systems without steady states. Our decomposition leads to far-from-equilibrium thermodynamic uncertainty relations and speed limits. As an illustration, we derive a thermodynamic bound on the time necessary for one cycle in a chemical oscillator.

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arXiv2022

Information-geometric structure for chemical thermodynamics: An explicit construction of dual affine coordinates

We construct an information-geometric structure for chemical thermodynamics, applicable to a wide range of chemical reaction systems including non-ideal and open systems. For this purpose, we explicitly construct dual affine coordinate systems, which completely designate an information-geometric structure, using the extent of reactions and the affinities of reactions as coordinates on a linearly-constrained space of amounts of substances. The resulting structure induces a metric and a divergence (a function of two distributions of amounts), both expressed with chemical potentials. These quantities have been partially known for ideal-dilute solutions, but their extensions for non-ideal solutions and the complete underlying structure are novel. The constructed geometry is a generalization of dual affine coordinates for stochastic thermodynamics. For example, the metric and the divergence are generalizations of the Fisher information and the Kullback-Leibler divergence. As an application, we identify the chemical-thermodynamic analog of the Hatano-Sasa excess entropy production using our divergence.

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arXiv2022

Thermodynamic Uncertainty Relations for Steady-State Thermodynamics

A system can be driven out of equilibrium by both time-dependent and nonconservative forces, which gives rise to a decomposition of the dissipation into two non-negative components, called the excess and housekeeping entropy productions. We derive thermodynamic uncertainty relations for the excess and housekeeping entropy. These can be used as tools to estimate the individual components, which are in general difficult to measure directly. We introduce a decomposition of an arbitrary current into excess and housekeeping parts, which provide lower bounds on the respective entropy production. Furthermore, we also provide a geometric interpretation of the decomposition, and show that the uncertainties of the two components are not independent, but rather have to obey a joint uncertainty relation, which also yields a tighter bound on the total entropy production. We apply our results to two examples that illustrate the physical interpretation of the components of the current and how to estimate the entropy production.

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arXiv2022

Geometric decomposition of entropy production into excess, housekeeping and coupling parts

For a generic overdamped Langevin dynamics driven out of equilibrium by both time-dependent and nonconservative forces, the entropy production rate can be decomposed into two positive terms, termed excess and housekeeping entropy. However, this decomposition is not unique: There are two distinct decompositions, one due to Hatano and Sasa, the other one due to Maes and Netočny. Here, we establish the connection between these two decompositions and provide a simple, geometric interpretation. We show that this leads to a decomposition of the entropy production rate into three positive terms, which we call excess, housekeeping and coupling part, respectively. The coupling part characterizes the interplay between the time-dependent and nonconservative forces. We also derive thermodynamic uncertainty relations for the excess and housekeeping entropy in both the Hatano-Sasa and Maes-Netočny-decomposition and show that all quantities obey integral fluctuation theorems. We illustrate the decomposition into three terms using a solvable example of a dragged particle in a nonconservative force field.

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arXiv2022

Thermodynamic role of main reaction pathway and multi-body information flow in membrane transport

The two classes of membrane transport, namely, secondary active and passive transport, are understood as different reaction pathways in the same protein structure, described by the 16-state model in this paper. To quantify the thermodynamic difference between secondary active transport and passive transport, we extend the second law of information thermodynamics of the autonomous demon in the four-state model composed of two subsystems to the 16-state model composed of four subsystems representing the membrane transport. We reduce the 16 states to 4 states and derive the coarse-grained second law of information thermodynamics, which provides an upper bound of the free energy transport by the coarse-grained information flow. We also derive an upper bound on the free energy transport by the multi-body information flow representing the two-body or four-body correlations in the 16-state model by exploiting the cycle decomposition. The coarse-grained information flow and the multi-body information flows express the quantitative difference between secondary active and passive transport. The numerical analysis shows that the coarse-grained information flow is positive for secondary active transport and negative for passive transport. The four-body correlation is dominant in the multi-body information flows for secondary active transport. In contrast, the two-body correlation is dominant for passive transport. This result shows that both the sign of the coarse-grained information flow and the difference of the four-body correlation and the two-body correlation explain the difference of the free energy transport in secondary active and passive transport.

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arXiv2022

Geometric decomposition of entropy production in out-of-equilibrium systems

Two qualitatively different ways of driving a physical system out of equilibrium, time-dependent and non-conservative forcing, are reflected by the decomposition of the system's entropy production into excess and housekeeping parts. We show that the difference between these two types of driving gives rise to a geometric formulation in terms of two orthogonal contributions to the currents in the system. This geometric picture in a natural way leads to variational expressions for both the excess and housekeeping entropy, which allow calculating both contributions independently from the trajectory data of the system. We demonstrate this by calculating the excess and housekeeping entropy of a particle in a time-dependent, tilted periodic potential.

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arXiv2021

Information geometry, trade-off relations, and generalized Glansdorff-Prigogine criterion for stability

We discuss a relationship between information geometry and the Glansdorff-Prigogine criterion for stability. For the linear master equation, we found a relation between the line element and the excess entropy production rate. This relation leads to a new perspective of stability in a nonequilibrium steady-state. We also generalize the Glansdorff-Prigogine criterion for stability based on information geometry. Our information-geometric criterion for stability works well for the nonlinear master equation, where the Glansdorff-Prigogine criterion for stability does not work well. We derive a trade-off relation among the fluctuation of the observable, the mean change of the observable, and the intrinsic speed. We also derive a novel thermodynamic trade-off relation between the excess entropy production rate and the intrinsic speed. These trade-off relations provide a physical interpretation of our information-geometric criterion for stability. We illustrate our information-geometric criterion for stability by an autocatalytic reaction model, where dynamics are driven by a nonlinear master equation.

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