Generalized Green-Kubo relation and integral fluctuation theorem for driven dissipative systems without microscopic time reversibility

Softening and Residual Loss Modulus of Jammed Grains under Oscillatory Shear in an Absorbing State

From a theoretical study of the mechanical response of jammed materials comprising frictionless and overdamped particles under oscillatory shear, we find that the material becomes soft, and the loss modulus remains nonzero even in an absorbing state where any irreversible plastic deformation does not exist. The trajectories of the particles in this region exhibit hysteresis loops. We succeed in clarifying the origin of the softening of the material and the residual loss modulus with the aid of Fourier analysis. We also clarify the roles of the yielding point in the softening to distinguish the plastic deformation from reversible deformation in the absorbing state.

Tighter thermodynamic bound on the speed limit in systems with unidirectional transitions

We consider a general discrete state-space system with both unidirectional and bidirectional links. In contrast to bidirectional links, there is no reverse transition along the unidirectional links. Herein, we first compute the statistical length and the thermodynamic cost function for transitions in the probability space, highlighting contributions from total, environmental, and resetting (unidirectional) entropy production. Then we derive the thermodynamic bound on the speed limit to connect two distributions separated by a finite time, showing the effect of the presence of unidirectional transitions. Uncertainty relationships can be found for the temporal first and second moments of the average resetting entropy production. We derive simple expressions in the limit of slow unidirectional transition rates. Finally, we present a refinement of the thermodynamic bound by means of an optimization procedure. We numerically investigate these results on systems that stochastically reset with constant and periodic resetting rate.

Entropy in Cell Biology: Information Thermodynamics of a Binary Code and Szilard Engine Chain Model of Signal Transduction

A model of signal transduction from the perspective of informational thermodynamics has been reported in recent studies, and several important achievements have been obtained. The first achievement is that signal transduction can be modelled as a binary code system, in which two forms of signalling molecules are utilised in individual steps. The second is that the average entropy production rate is consistent during the signal transduction cascade when the signal event number is maximised in the model. The third is that a Szilard engine can be a single-step model in the signal transduction. This article reviews these achievements and further introduces a new chain of Szilard engines as a biological reaction cascade (BRC) model. In conclusion, the presented model provides a way of computing the channel capacity of a BRC.

Divergence of Viscosity in Jammed Granular Materials: A Theoretical Approach

A theory for jammed granular materials is developed with the aid of a nonequilibrium steady-state distribution function. The approximate nonequilibrium steady-state distribution function is explicitly given in the weak dissipation regime by means of the relaxation time. The theory quantitatively agrees with the results of the molecular dynamics simulation on the critical behavior of the viscosity below the jamming point without introducing any fitting parameter.

Simulation of cohesive fine powders under a plane shear

Three-dimensional molecular-dynamics simulations of cohesive dissipative powders under a plane shear are performed. We find the various phases depending on the dimensionless shear rate and the dissipation rate as well as the density. We also find that the shape of clusters depends on the initial condition of velocities of particles when the dissipation is large. Our simple stochastic model reproduces the non-Gaussian velocity distribution function appearing in the coexistence phase of a gas and a plate.

Response function of turbulence computed via fluctuation-response relation of a Langevin system with vanishing noise

For a shell model of the fully developed turbulence and the incompressible Navier-Stokes equations in the Fourier space, when a Gaussian white noise is artificially added to the equation of each mode, an expression of the mean linear response function in terms of the velocity correlation functions is derived by applying the method developed for nonequilibrium Langevin systems [Harada and Sasa, Phys. Rev. Lett. 95, 130602 (2005)]. We verify numerically for the shell-model case that the derived expression of the response function, as the noise tends to zero, converges to the response function of the noiseless shell model.

Effect of elastic vibrations on normal head-on collisions of isothermal spheres

We numerically investigate head-on collisions of isothermal viscoelastic spheres. We find that the restitution coefficient oscillates against the impact speed if the solid viscosity inside the sphere is small enough. We confirm that the oscillation arises from the resonance between the duration of contact and the eigenfrequencies of the sphere. This oscillation disappears if there exists the strong solid viscosity in spheres. We also find that a sinusoidal behavior of the restitution coefficient against the initial phase in the eigenmodes for collisions between a thermally activated sphere and a flat wall. As a result, the restitution coefficient can exceed unity if the impact speed of the colliding sphere is nearly equal to or slower than the thermal speed. We have confirmed the existence of the fluctuation theorem for impact processes through our simulation.

Nonequilibrium identities and response theory for dissipative particles

We derive some nonequilibrium identities such as the integral fluctuation theorem and the Jarzynski equality starting from a nonequilibrium state for dissipative classical systems. Thanks to the existence of the integral fluctuation theorem we can naturally introduce an entropy-like quantity for dissipative classical systems in far from equilibrium states. We also derive the generalized Green-Kubo formula as a nonlinear response theory for a steady dynamics around a nonequilibrium state. We numerically verify the validity of the derived formulas for sheared frictionless granular particles.

Probing small-scale intermittency with a fluctuation theorem

We characterize statistical properties of the flow field in developed turbulence using concepts from stochastic thermodynamics. On the basis of data from a free air-jet experiment, we demonstrate how the dynamic fluctuations induced by small-scale intermittency generate analogs of entropy-consuming trajectories with sufficient weight to make fluctuation theorems observable at the macroscopic scale. We propose an integral fluctuation theorem for the entropy production associated with the stochastic evolution of velocity increments along the eddy hierarchy and demonstrate its extreme sensitivity to the accurate description of the tails of the velocity distributions.

Stochastic thermodynamics, fluctuation theorems and molecular machines

Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics such as work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. For a basic Markovian dynamics implemented either on the continuum level with Langevin equations or on a discrete set of states as a master equation, thermodynamic consistency imposes a local-detailed balance constraint on noise and rates, respectively. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation-dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production.

Entropy production in nonequilibrium steady states: a different approach and an exactly solvable canonical model

We discuss entropy production in nonequilibrium steady states by focusing on paths obtained by sampling at regular (small) intervals, instead of sampling on each change of the system's state. This allows us to directly study entropy production in systems with microscopic irreversibility. The two sampling methods are equivalent otherwise, and the fluctuation theorem also holds for the different paths. We focus on a fully irreversible three-state loop, as a canonical model of microscopic irreversibility, finding its entropy distribution, rate of entropy production, and large deviation function in closed analytical form, and showing that the observed kink in the large deviation function arises solely from microscopic irreversibility.