arXiv subjects

Naoko Nakagawa

Publications and source records attributed to Naoko Nakagawa.

At least 37 records · Page 2Linked to original sources

arXiv2016

Numerical examination of steady-state thermodynamics from the entropy connected to the excess heat

We numerically determine the entropy for heat-conducting states, which is connected to the so-called excess heat considered as a basic quantity for steady-state thermodynamics in nonequilibrium. We adopt an efficient method to estimate the entropy from the bare heat current and find that the obtained entropy agrees with the familiar local equilibrium hypothesis well. Our method possesses a wider applicability than local equilibrium and opens a possibility to compare thermodynamic properties of complex systems with those in the local equilibrium. We further investigate the entropy for heat-conducting states and find that it exhibits both extensive and additive properties; however, the two properties do not degenerate each other differently from those at equilibrium. The separation of the extensivity and additivity makes it difficult to apply powerful thermodynamic methods.

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arXiv2014

Exact equalities and thermodynamic relations for nonequilibrium steady states

We study thermodynamic operations which bring a nonequilibrium steady state (NESS) to another NESS in physical systems under nonequilibrium conditions. We model the system by a suitable Markov jump process, and treat thermodynamic operations as protocols according to which the external agent varies parameters of the Markov process. Then we prove, among other relations, a NESS version of the Jarzynski equality and the extended Clausius relation. The latter can be a starting point of thermodynamics for NESS. We also find that the corresponding nonequilibrium entropy has a microscopic representation in terms of symmetrized Shannon entropy in systems where the microscopic description of states involves "momenta". All the results in the present paper are mathematically rigorous.

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arXiv2014

Universal expression for adiabatic pumping in terms of non-equilibrium steady states

We develop a unified treatment of pumping and nonequilibrium thermodynamics. We show that the pumping current generated through an adiabatic mechanical operation in equilibrium can be expressed in terms of the stationary distribution of the corresponding driven nonequilibrium system. We also show that the total transfer in pumping can be evaluated from the work imported to the driven counterpart. These findings lead us to a unified viewpoint for pumping and nonequilibrium thermodynamics.

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arXiv2014

Characterization of the low temperature properties of a simplified protein model

Prompted by results that showed that a simple protein model, the frustrated Gō model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature properties of proteins. First, we examine equilibrium fluctuations. We calculate its incoherent neutron-scattering structure factor and show that it can be well described by a theory using the one-phonon approximation. By performing an inherent structure analysis, we assess the transitions among energy states at low temperatures. Then, we examine non-equilibrium fluctuations after a sudden cooling of the protein. We investigate the violation of the fluctuation--dissipation theorem in order to analyze the protein glass transition. We find that the effective temperature of the quenched protein deviates from the temperature of the thermostat, however it relaxes towards the actual temperature with an Arrhenius behavior as the waiting time increases. These results of the equilibrium and non-equilibrium studies converge to the conclusion that the apparent dynamical transition of this coarse-grained model cannot be attributed to a glassy behavior.

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arXiv2013

Work relations for time-dependent states

For time-dependent states generated by an external operation, a generalized free energy may be introduced by the relative entropy with respect to an equilibrium state realized after sufficient relaxation from the time-dependent states. Recently, by studying over-damped systems, Sivak and Crooks presented a formula that relates the generalized free energy with measurable thermodynamic works. We re-derive this relation with emphasizing a connection to an extended Clausius relation proposed in the framework of steady state thermodynamics. As a natural consequence, we generalize this relation to be valid for systems with momentum degrees of freedom, where the Shannon entropy in the generalized free energy is replaced by a symmetric one.

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arXiv2013

Conformational Temperature Characterizing the Folding of a Protein

The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for inherent structures are introduced and from these quantities a conformational temperature is defined. The conformational temperature follows the time evolution of a slow relaxation process and reaches the bath temperature when the system is equilibrated. We show that the nonequilibrium system is described by two temperatures, one for fast vibration and the other for slow configurational relaxation, while the equilibrium system is by one temperature. The proposed formalism is applicable widely for the systems with many metastable states.

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arXiv2012

Work Relation and the Second Law of Thermodynamics in Nonequilibrium Steady States

We extend Jarzynski's work relation and the second law of thermodynamics to a heat conducting system which is operated by an external agent. These extensions contain a new non equilibrium contribution expressed as the violation of the (linear) response relation caused by the operation. We find that a natural extension of the minimum work principle involves information about the time-reversed operation, and is far from straightforward. Our work relation may be tested experimentally especially when the temperature gradient is small.

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arXiv2010

Entropy and Nonlinear Nonequilibrium Thermodynamic Relation for Heat Conducting Steady States

Among various possible routes to extend entropy and thermodynamics to nonequilibrium steady states (NESS), we take the one which is guided by operational thermodynamics and the Clausius relation. In our previous study, we derived the extended Clausius relation for NESS, where the heat in the original relation is replaced by its "renormalized" counterpart called the excess heat, and the Gibbs-Shannon expression for the entropy by a new symmetrized Gibbs-Shannon-like expression. Here we concentrate on Markov processes describing heat conducting systems, and develop a new method for deriving thermodynamic relations. We first present a new simpler derivation of the extended Clausius relation, and clarify its close relation with the linear response theory. We then derive a new improved extended Clausius relation with a "nonlinear nonequilibrium" contribution which is written as a correlation between work and heat. We argue that the "nonlinear nonequilibrium" contribution is unavoidable, and is determined uniquely once we accept the (very natural) definition of the excess heat. Moreover it turns out that to operationally determine the difference in the nonequilibrium entropy to the second order in the temperature difference, one may only use the previous Clausius relation without a nonlinear term or must use the new relation, depending on the operation (i.e., the path in the parameter space). This peculiar "twist" may be a clue to a better understanding of thermodynamics and statistical mechanics of NESS.

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arXiv2009

Critical examination of the inherent-structure-landscape analysis of two-state folding proteins

Recent studies attracted the attention on the inherent structure landscape (ISL) approach as a reduced description of proteins allowing to map their full thermodynamic properties. However, the analysis has been so far limited to a single topology of a two-state folding protein, and the simplifying assumptions of the method have not been examined. In this work, we construct the thermodynamics of four two-state folding proteins of different sizes and secondary structure by MD simulations using the ISL method, and critically examine possible limitations of the method. Our results show that the ISL approach correctly describes the thermodynamics function, such as the specific heat, on a qualitative level. Using both analytical and numerical methods, we show that some quantitative limitations cannot be overcome with enhanced sampling or the inclusion of harmonic corrections.

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arXiv2008

Representation of nonequilibrium steady states in large mechanical systems

Recently a novel concise representation of the probability distribution of heat conducting nonequilibrium steady states was derived. The representation is valid to the second order in the ``degree of nonequilibrium'', and has a very suggestive form where the effective Hamiltonian is determined by the excess entropy production. Here we extend the representation to a wide class of nonequilibrium steady states realized in classical mechanical systems where baths (reservoirs) are also defined in terms of deterministic mechanics. The present extension covers such nonequilibrium steady states with a heat conduction, with particle flow (maintained either by external field or by particle reservoirs), and under an oscillating external field. We also simplify the derivation and discuss the corresponding representation to the full order.

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arXiv2008

Steady State Thermodynamics for Heat Conduction -- Microscopic Derivation

Starting from microscopic mechanics, we derive thermodynamic relations for heat conducting nonequilibrium steady states. The extended Clausius relation enables one to experimentally determine nonequilibrium entropy to the second order in the heat current. The associated Shannon-like microscopic expression of the entropy is suggestive. When the heat current is fixed, the extended Gibbs relation provides a unified treatment of thermodynamic forces in linear nonequilibrium regime.

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arXiv2007

An expression for stationary distribution in nonequilibrium steady state

We study the nonequilibrium steady state realized in a general stochastic system attached to multiple heat baths and/or driven by an external force. Starting from the detailed fluctuation theorem we derive concise and suggestive expressions for the corresponding stationary distribution which are correct up to the second order in thermodynamic forces. The probability of a microstate $η$ is proportional to $\exp[Φ(η)]$ where $Φ(η)=-\sum_kβ_k\mathcal{E}_k(η)$ is the excess entropy change. Here $\mathcal{E}_k(η)$ is the difference between two kinds of conditioned path ensemble averages of excess heat transfer from the $k$-th heat bath whose inverse temperature is $β_k$. Our expression may be verified experimentally in nonequilibrium states realized, for example, in mesoscopic systems.

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arXiv2007

A Reversibility Parameter for a Markovian Stepper

Recent experimental studies on the stepwize motion of biological molecular motors have revealed that the ``characteristic distance'' of a step is usually less than the actual step size. This observation implies that the detailed-balance condition for kinetic rates of steps is violated in these motors. In this letter, in order to clarify the significance of the characteristic distance, we study a Langevin model of a molecular motor with a hidden degree of freedom. We find that the ratio of the characteristic distance to the step size is equal to unity if the dominant paths in the state space are one dimensional, while it deviates from unity if the dominant paths are branched. Therefore, this parameter can be utilized to determine the reversibility of a motor even under a restricted observation.

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arXiv2006

Hidden heat transfer in equilibrium states implies directed motion in nonequilibrium states

We study a class of heat engines including Feynman's ratchet, which exhibits a directed motion of a particle in nonequilibrium steady states maintained by two heat baths. We measure heat transfer from each heat bath separately, and average them using a careful procedure that reveals the nature of the heat transfer associated with directed steps of the particle. Remarkably we find that steps are associated with nonvanishing heat transfer even in equilibrium, and there is a quantitative relation between this ``hidden heat transfer'' and the directed motion of the particle. This relation is clearly understood in terms of the ``principle of heat transfer enhancement'', which is expected to apply to a large class of highly nonequilibrium systems.

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arXiv2006

A heat pump at a molecular scale controlled by a mechanical force

We show that a mesoscopic system such as Feynman's ratchet may operate as a heat pump, and clarify a underlying physical picture. We consider a system of a particle moving along an asymmetric periodic structure . When put into a contact with two distinct heat baths of equal temperature, the system transfers heat between two baths as the particle is dragged. We examine Onsager relation for the heat flow and the particle flow, and show that the reciprocity coefficient is a product of the characteristic heat and the diffusion constant of the particle. The characteristic heat is the heat transfer between the baths associated with a barrier-overcoming process. Because of the correlation between the heat flow and the particle flow, the system can work as a heat pump when the particle is dragged. This pump is particularly effective at molecular scales where the energy barrier is of the order of the thermal energy.

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arXiv2004

An oriented process induced by dynamically regulated energy barriers

A novel mechanism for the appearance of oriented processes is investigated with a flexible dynamical system overcoming barriers. Under non-equilibrium condition with external driving, reaction paths deviate from that at equilibrium with an accompanying violation of symmetry between the forward and the reverse paths. Although we never introduce any external switching of potentials to generate the oriented processes, multi-dimensional flexible dynamics promote the oriented processes through this symmetry violation. Along the reaction paths, bottleneck points are proposed as a rate-controlling factor, which determine the {\it direction-dependent activation energies} satisfying Arrhenius-like law for the rate constants. In comparison, in stiff systems, the oriented process is suggested to appear in different manner from this scenario.

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arXiv2003

Autonomous Energy Transducer: Proposition, Example, Basic Characteristics

We propose a concept of autonomous energy transducer at a molecular scale, where output is produced with small input energy, of the same order of the thermal energy, without restriction of magnitude or timing of input, and without any control after the input. As an example that satisfies these requisites, a dynamical systems model with several degrees of freedom is proposed, which transduces input energy to output motion on the average. It is shown that this transduction is robust and the coupling between the input and output is generally loose. How this transducer works is analyzed in terms of dynamical systems theory, where chaotic dynamics of the internal degrees of freedom, as well as duration of active state which is self-organized with the energy flow, is essential. We also discuss possible relationships to enzyme dynamics or protein motors.

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arXiv2002

A Dynamic Mechanism of Energy Conversion to a Mechanical Work

We propose a dynamic mechanism of a molecular machine for energy conversion, by considering a simple model describing the dynamics of two components, the head and the chain. After injection of energy to the head region, the energy is stored at one part for some time, and is used step by step, allowing the head to move directionally along the chain, irrespectively of the direction of the input, under a fluctuating environment. Our system can adjust the timing with which the head crosses the energy barrier by taking advantage of internal dynamics and the flexibility of components. The mechanism is shown to be robust and efficient. Some suggestions are given for molecular machines.

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