References of "PHYSICAL REVIEW E"
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See detailThermodynamic cycles with active matter
Ekeh, Timothy; Cates, Michael E.; Fodor, Etienne UL

in PHYSICAL REVIEW E (2020), 102(1),

Active matter constantly dissipates energy to power the self-propulsion of its microscopic constituents. This opens the door to designing innovative cyclic engines without any equilibrium equivalent. We ... [more ▼]

Active matter constantly dissipates energy to power the self-propulsion of its microscopic constituents. This opens the door to designing innovative cyclic engines without any equilibrium equivalent. We offer a consistent thermodynamic framework to characterize and optimize the performances of such cycles. Based on a minimal model, we put forward a protocol which extracts work by controlling only the properties of the confining walls at boundaries, and we rationalize the transitions between optimal cycles. We show that the corresponding power and efficiency are generally proportional, so that they reach their maximum values at the same cycle time in contrast with thermal cycles, and we provide a generic relation constraining the fluctuations of the power. [less ▲]

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See detailLandau-Zener Lindblad equation and work extraction from coherences
Thingna, J.; Esposito, Massimiliano UL; Barra, F.

in Physical Review E (2019), 99(4),

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See detailOptimizing active work: Dynamical phase transitions, collective motion and jamming
Nemoto, Takahiro; Fodor, Etienne UL; Cates, Michael E. et al

in PHYSICAL REVIEW E (2019), 99(2),

Active work measures how far the local self-forcing of active particles translates into real motion. Using population Monte Carlo methods, we investigate large deviations in the active work for repulsive ... [more ▼]

Active work measures how far the local self-forcing of active particles translates into real motion. Using population Monte Carlo methods, we investigate large deviations in the active work for repulsive active Brownian disks Minimizing the active work generically results in dynamical arrest; in contrast, despite the lack of aligning interactions, trajectories of high active work correspond to a collectively moving, aligned state. We use heuristic and analytic arguments to explain the origin of dynamical phase transitions separating the arrested, typical, and aligned regimes. [less ▲]

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See detailNon-Markovianity and negative entropy production rates
Strasberg, P.; Esposito, Massimiliano UL

in Physical Review E (2019), 99(1),

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See detailNon-Gaussian noise without memory in active matter
Fodor, Etienne UL; Hayakawa, Hisao; Tailleur, Julien et al

in PHYSICAL REVIEW E (2018), 98(6),

Modeling the dynamics of an individual active particle invariably involves an isotropic noisy self-propulsion component, in the form of run-and-tumble motion or variations around it. This nonequilibrium ... [more ▼]

Modeling the dynamics of an individual active particle invariably involves an isotropic noisy self-propulsion component, in the form of run-and-tumble motion or variations around it. This nonequilibrium source of noise is neither white-there is persistence-nor Gaussian. While emerging collective behavior in active matter has hitherto been attributed to the persistent ingredient, we focus on the non-Gaussian ingredient of self-propulsion. We show that by itself, that is, without invoking any memory effect, it is able to generate particle accumulation close to boundaries and effective attraction between otherwise repulsive particles, a mechanism which generically leads to motility-induced phase separation in active matter. [less ▲]

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See detailKinetics and thermodynamics of a driven open quantum system
Thingna, J.; Barra, F.; Esposito, Massimiliano UL

in Physical Review E (2017), 96(5),

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See detailActive cage model of glassy dynamics
Fodor, Etienne UL; Hayakawa, Hisao; Visco, Paolo et al

in PHYSICAL REVIEW E (2016), 94(1),

We build up a phenomenological picture in terms of the effective dynamics of a tracer confined in a cage experiencing random hops to capture some characteristics of glassy systems. This minimal ... [more ▼]

We build up a phenomenological picture in terms of the effective dynamics of a tracer confined in a cage experiencing random hops to capture some characteristics of glassy systems. This minimal description exhibits scale invariance properties for the small-displacement distribution that echo experimental observations. We predict the existence of exponential tails as a crossover between two Gaussian regimes. Moreover, we demonstrate that the onset of glassy behavior is controlled only by two dimensionless numbers: the number of hops occurring during the relaxation of the particle within a local cage and the ratio of the hopping length to the cage size. [less ▲]

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See detailFluctuating currents in stochastic thermodynamics. II. Energy conversion and nonequilibrium response in kinesin models
Altaner, Bernhard; Wachtel, Artur UL; Vollmer, Jürgen

in PHYSICAL REVIEW E (2015), 92(4), 042133

Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic thermodynamics uses Markovian jump processes to model the random transitions between ... [more ▼]

Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational states of these biological macromolecules. A recently developed theoretical framework [A. Wachtel, J. Vollmer, and B. Altaner, Phys. Rev. E 92, 042132 (2015)] provides a simple algorithm for the determination of macroscopic currents and correlation integrals of arbitrary fluctuating currents. Here we use it to discuss energy conversion and nonequilibrium response in different models for the molecular motor kinesin. Methodologically, our results demonstrate the effectiveness of the algorithm in dealing with parameter-dependent stochastic models. For the concrete biophysical problem our results reveal two interesting features in experimentally accessible parameter regions: the validity of a nonequilibrium Green-Kubo relation at mechanical stalling as well as a negative differential mobility for superstalling forces. [less ▲]

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See detailModeling the dynamics of a tracer particle in an elastic active gel
Ben-Isaac, E.; Fodor, Etienne UL; Visco, P. et al

in PHYSICAL REVIEW E (2015), 92(1),

The internal dynamics of active gels both in artificial (in vitro) model systems and inside the cytoskeleton of living cells has been extensively studied with experiments of recent years. These dynamics ... [more ▼]

The internal dynamics of active gels both in artificial (in vitro) model systems and inside the cytoskeleton of living cells has been extensively studied with experiments of recent years. These dynamics are probed using tracer particles embedded in the network of biopolymers together with molecular motors, and distinct nonthermal behavior is observed. We present a theoretical model of the dynamics of a trapped active particle, which allows us to quantify the deviations from equilibrium behavior, using both analytic and numerical calculations. We map the different regimes of dynamics in this system and highlight the different manifestations of activity: breakdown of the virial theorem and equipartition, different elasticity-dependent ``effective temperatures,'' and distinct non-Gaussian distributions. Our results shed light on puzzling observations in active gel experiments and provide physical interpretation of existing observations, as well as predictions for future studies. [less ▲]

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See detailLocal search methods based on variable focusing for random K-satisfiability
Lemoy, Rémi UL; Alava, Mikko; Aurell, Erik

in PHYSICAL REVIEW E (2015), 91(1), 013305-6

We introduce variable focused local search algorithms for satisfiabiliity problems. Usual approaches focus uniformly on unsatisfied clauses. The methods described here work by focusing on random variables ... [more ▼]

We introduce variable focused local search algorithms for satisfiabiliity problems. Usual approaches focus uniformly on unsatisfied clauses. The methods described here work by focusing on random variables in unsatisfied clauses. Variants are considered where variables are selected uniformly and randomly or by introducing a bias towards picking variables participating in several unsatistified clauses. These are studied in the case of the random 3-SAT problem, together with an alternative energy definition, the number of variables in unsatisfied constraints. The variable-based focused Metropolis search (V-FMS) is found to be quite close in performance to the standard clause-based FMS at optimal noise. At infinite noise, instead, the threshold for the linearity of solution times with instance size is improved by picking preferably variables in several UNSAT clauses. Consequences for algorithmic design are discussed. [less ▲]

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See detailFluctuating currents in stochastic thermodynamics. I. Gauge invariance of asymptotic statistics
Wachtel, Artur UL; Vollmer, Jürgen; Altaner, Bernhard

in PHYSICAL REVIEW E (2015), 92(4), 042132

Stochastic thermodynamics uses Markovian jump processes to model random transitions between observable mesoscopic states. Physical currents are obtained from antisymmetric jump observables defined on the ... [more ▼]

Stochastic thermodynamics uses Markovian jump processes to model random transitions between observable mesoscopic states. Physical currents are obtained from antisymmetric jump observables defined on the edges of the graph representing the network of states. The asymptotic statistics of such currents are characterized by scaled cumulants. In the present work, we use the algebraic and topological structure of Markovian models to prove a gauge invariance of the scaled cumulant-generating function. Exploiting this invariance yields an efficient algorithm for practical calculations of asymptotic averages and correlation integrals. We discuss how our approach generalizes the Schnakenberg decomposition of the average entropy-production rate, and how it unifies previous work. The application of our results to concrete models is presented in an accompanying publication. [less ▲]

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See detailUniversal theory of efficiency fluctuations
Verley, Gatien; Willaert, Tim; Van den Broeck, Christian et al

in Physical Review E (2014), 90(5),

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See detailEnergetics of active fluctuations in living cells
Fodor, Etienne UL; Kanazawa, K.; Hayakawa, H. et al

in PHYSICAL REVIEW E (2014), 90(4),

The nonequilibrium activity taking place in a living cell can be monitored with a tracer embedded in the medium. While microrheology experiments based on optical manipulation of such probes have become ... [more ▼]

The nonequilibrium activity taking place in a living cell can be monitored with a tracer embedded in the medium. While microrheology experiments based on optical manipulation of such probes have become increasingly standard, we put forward a number of experiments with alternative protocols that, we claim, will provide insight into the energetics of active fluctuations. These are based on either performing thermodynamiclike cycles in control-parameter space or determining response to external perturbations of the confining trap beyond simple translation. We illustrate our proposals on an active itinerant Brownian oscillator modeling the dynamics of a probe embedded in a living medium. [less ▲]

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See detailStochastically driven single-level quantum dot: A nanoscale finite-time thermodynamic machine and its various operational modes
Esposito, Massimiliano UL; Kumar, Niraj; Lindenberg, Katja et al

in Physical Review E (2012), 85(3),

We describe a single-level quantum dot in contact with two leads as a nanoscale finite-time thermodynamic machine. The dot is driven by an external stochastic force that switches its energy between two ... [more ▼]

We describe a single-level quantum dot in contact with two leads as a nanoscale finite-time thermodynamic machine. The dot is driven by an external stochastic force that switches its energy between two values. In the isothermal regime, it can operate as a rechargeable battery by generating an electric current against the applied bias in response to the stochastic driving and then redelivering work in the reverse cycle. This behavior is reminiscent of the Parrondo paradox. If there is a thermal gradient the device can function as a work-generating thermal engine or as a refrigerator that extracts heat from the cold reservoir via the work input of the stochastic driving. The efficiency of the machine at maximum power output is investigated for each mode of operation, and universal features are identified. [less ▲]

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See detailStochastic thermodynamics under coarse graining
Esposito, Massimiliano UL

in Physical Review E (2012), 85(4),

A general formulation of stochastic thermodynamics is presented for open systems exchanging energy and particles with multiple reservoirs. By introducing a partition in terms of “mesostates” (e.g., sets ... [more ▼]

A general formulation of stochastic thermodynamics is presented for open systems exchanging energy and particles with multiple reservoirs. By introducing a partition in terms of “mesostates” (e.g., sets of “microstates”), the consequence on the thermodynamic description of the system is studied in detail. When microstates within mesostates rapidly thermalize, the entire structure of the microscopic theory is recovered at the mesostate level. This is not the case when these microstates remain out of equilibrium, leading to additional contributions to the entropy balance. Some of our results are illustrated for a model of two coupled quantum dots. [less ▲]

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See detailThermodynamics of a stochastic twin elevator
Kumar, Niraj; Van den Broeck, Christian; Esposito, Massimiliano UL et al

in Physical Review E (2011), 84(5),

We study the nonequilibrium thermodynamics of a single particle with two available energy levels, in contact with a classical (Maxwell-Boltzmann) or quantum (Bose-Einstein) heat bath. The particle can ... [more ▼]

We study the nonequilibrium thermodynamics of a single particle with two available energy levels, in contact with a classical (Maxwell-Boltzmann) or quantum (Bose-Einstein) heat bath. The particle can undergo transitions between the levels via thermal activation or deactivation. The energy levels are alternately raised at a given rate regardless of occupation by the particle, maintaining a fixed energy gap equal to ε between them. We explicitly calculate the work, heat, and entropy production rates. The efficiency in both the classical and the quantum case goes to a limit between 100 and 50% that depends on the relative rates of particle transitions and level elevation. In the classical problem we explicitly find the large deviation functions for heat, work, and internal energy. [less ▲]

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See detailThree faces of the second law. II. Fokker-Planck formulation
Van den Broeck, Christian; Esposito, Massimiliano UL

in Physical Review E (2010), 82(1),

The total entropy production is the sum of two contributions, the so-called adiabatic and nonadiabatic entropy productions, each of which is non-negative. We derive their explicit expressions for ... [more ▼]

The total entropy production is the sum of two contributions, the so-called adiabatic and nonadiabatic entropy productions, each of which is non-negative. We derive their explicit expressions for continuous Markovian processes, discuss their properties, and illustrate their behavior on two exactly solvable models. [less ▲]

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See detailThree faces of the second law. I. Master equation formulation
Esposito, Massimiliano UL; Van den Broeck, Christian

in Physical Review E (2010), 82(1),

We propose a formulation of stochastic thermodynamics for systems subjected to nonequilibrium constraints i.e. broken detailed balance at steady state and furthermore driven by external time-dependent ... [more ▼]

We propose a formulation of stochastic thermodynamics for systems subjected to nonequilibrium constraints i.e. broken detailed balance at steady state and furthermore driven by external time-dependent forces. A splitting of the second law occurs in this description leading to three second-law-like relations. The general results are illustrated on specific solvable models. The present paper uses a master equation based approach. [less ▲]

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See detailQuantum-dot Carnot engine at maximum power
Esposito, Massimiliano UL; Kawai, Ryoichi; Lindenberg, Katja et al

in Physical Review E (2010), 81(4),

We evaluate the efficiency at maximum power of a quantum-dot Carnot heat engine. The universal values of the coefficients at the linear and quadratic order in the temperature gradient are reproduced ... [more ▼]

We evaluate the efficiency at maximum power of a quantum-dot Carnot heat engine. The universal values of the coefficients at the linear and quadratic order in the temperature gradient are reproduced. Curzon-Ahlborn efficiency is recovered in the limit of weak dissipation. [less ▲]

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See detailPulse propagation in decorated granular chains: An analytical approach
Harbola, Upendra; Rosas, Alexandre; Romero, Aldo H. et al

in Physical Review E (2009), 80(5),

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