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Driven probe under harmonic confinement in a colloidal bath ; Fodor, Etienne in Journal of Statistical Mechanics: Theory and Experiment (2019) Colloids held by optical or magnetic tweezers have been used to explore the local rheological properties of a complex medium and to extract work from fluctuations with some appropriate protocols. However ... [more ▼] Colloids held by optical or magnetic tweezers have been used to explore the local rheological properties of a complex medium and to extract work from fluctuations with some appropriate protocols. However, a general theoretical understanding of the interplay between the confinement and the interaction with the environment is still lacking. Here, we explore the statistical properties of the position of a probe confined in a harmonic trap moving at constant velocity and interacting with a bath of colloidal particles maintained at a different temperature. Interactions among particles are accounted for by a systematic perturbation, whose range of validity is tested against direct simulations of the full dynamics. Overall, our results provide a way to predict the effect of the driving and the environment on the probe, and can potentially be used to investigate the properties of colloidal heat engines with many-body interactions. [less ▲] Detailed reference viewed: 11 (3 UL)Thermodynamics of accuracy in kinetic proofreading: dissipation and efficiency trade-offs Rao, Riccardo ; in Journal of Statistical Mechanics: Theory and Experiment (2015) The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e. by a mechanism which reduces the error rate of the information-handling process by ... [more ▼] The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e. by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide a consistent thermodynamic description of enzyme-assisted assembly processes involving competing substrates, in a master equation framework. We introduce and evaluate a measure of the efficiency based on rigorous non- equilibrium inequalities. The performance of several proofreading models are thus analyzed and the related time, dissipation and efficiency versus error trade-offs exhibited for different discrimination regimes. We finally introduce and analyse in the same framework a simple model which takes into account correlations between consecutive enzyme-assisted assembly steps. This work highlights the relevance of the distinction between energetic and kinetic discrimination regimes in enzyme-substrate interactions. [less ▲] Detailed reference viewed: 161 (8 UL)Mutual entropy production in bipartite systems Diana, Giovanni ; Esposito, Massimiliano in Journal of Statistical Mechanics: Theory and Experiment (2014) It was recently shown by Barato et al (2013 Phys. Rev. E 87 042104) that the mutual information at the trajectory level of a bipartite Markovian system is not bounded by the entropy production. In the ... [more ▼] It was recently shown by Barato et al (2013 Phys. Rev. E 87 042104) that the mutual information at the trajectory level of a bipartite Markovian system is not bounded by the entropy production. In the same way as Gaspard showed (2004 J. Stat. Phys. 117 599) that the entropy production is not directly related to the Shannon entropy at the trajectory level but is in fact equal to its difference from the so-called time-reversed Shannon entropy, we show in this paper that the difference between the mutual information and its time-reversed form is equal to the mutual entropy production (MEP), i.e. the difference between the full entropy production and that of the two marginal processes. Evaluation of the MEP is in general a difficult task due to non-Markovian effects. For bipartite systems, we provide closed expressions in various limiting regimes which we verify by numerical simulations. [less ▲] Detailed reference viewed: 166 (7 UL)Financial interaction networks inferred from traded volumes ; Lemoy, Rémi ; in Journal of Statistical Mechanics: Theory and Experiment (2014) In order to use the advanced inference techniques available for Ising models, we transform complex data (real vectors) into binary strings, using local averaging and thresholding. This transformation ... [more ▼] In order to use the advanced inference techniques available for Ising models, we transform complex data (real vectors) into binary strings, using local averaging and thresholding. This transformation introduces parameters, which must be varied to characterize the behaviour of the system. The approach is illustrated on financial data, using three inference methods-equilibrium, synchronous and asynchronous inference-to construct functional connections between stocks. We show that the traded volume information is enough to obtain well-known results about financial markets that use, however, presumably richer price information: collective behaviour ('market mode') and strong interactions within industry sectors. Synchronous and asynchronous Ising inference methods give results that are coherent with equilibrium ones and are more detailed since the obtained interaction networks are directed. [less ▲] Detailed reference viewed: 96 (1 UL)Transient fluctuation theorems for the currents and initial equilibrium ensembles Polettini, Matteo ; Esposito, Massimiliano in Journal of Statistical Mechanics: Theory and Experiment (2014) Detailed reference viewed: 58 (3 UL)Generally covariant state-dependent diffusion Polettini, Matteo in Journal of Statistical Mechanics: Theory and Experiment (2013), (07), Statistical invariance of Wiener increments under SO(n) rotations provides a notion of gauge transformation of state-dependent Brownian motion. We show that the stochastic dynamics of non-gauge-invariant ... [more ▼] Statistical invariance of Wiener increments under SO(n) rotations provides a notion of gauge transformation of state-dependent Brownian motion. We show that the stochastic dynamics of non-gauge-invariant systems is not unambiguously defined. They typically do not relax to equilibrium steady states even in the absence of external forces. Assuming both coordinate covariance and gauge invariance, we derive a second-order Langevin equation with state-dependent diffusion matrix and vanishing environmental forces. It differs from previous proposals but nevertheless incorporates the Einstein relation, a Maxwellian conditional steady state for the velocities, and the equipartition theorem. The overdamping limit leads to a stochastic differential equation in state space that cannot be interpreted as a pure differential (Itō, Stratonovich or other). At odds with the latter interpretations, the corresponding Fokker–Planck equation admits an equilibrium steady state; a detailed comparison with other theories of state-dependent diffusion is carried out. We propose this as a theory of diffusion in a heat bath with varying temperature. Besides equilibrium, a crucial experimental signature is the nonuniform steady spatial distribution. [less ▲] Detailed reference viewed: 159 (4 UL)Entropy production in quantum Brownian motion ; Esposito, Massimiliano ; in Journal of Statistical Mechanics: Theory and Experiment (2013), P04005 We investigate how to coherently define entropy production for a process of transient relaxation in the quantum Brownian motion model for the harmonic potential. We compare a form, referred to as ‘poised’ ... [more ▼] We investigate how to coherently define entropy production for a process of transient relaxation in the quantum Brownian motion model for the harmonic potential. We compare a form, referred to as ‘poised’ (P), which after non-Markovian transients corresponds to a definition of heat as the change in the system Hamiltonian of mean force, with a recent proposal by Esposito et al (ELB) based on a definition of heat as the energy change in the bath. Both expressions yield a positive-definite entropy production and they coincide for vanishing coupling strength, but their difference is proved to be always positive (after non-Markovian transients disappear) and to grow as the coupling strength increases. In the classical ver-damped limit the ‘poised’ entropy production converges to the entropy production used in stochastic thermodynamics. We also investigate the effects of the system size, and of the ensuing Poincar´e recurrences, and how the classical limit is approached. We close by discussing the strongcoupling limit, in which the ideal canonical equilibrium of the bath is violated. [less ▲] Detailed reference viewed: 153 (6 UL)Dynamical fluctuations in a simple housing market model Lemoy, Rémi ; in Journal of Statistical Mechanics: Theory and Experiment (2012) We consider a simple stochastic model of an urban rental housing market, in which the interaction of tenants and landlords induces rent fluctuations. We simulate the model numerically and measure the ... [more ▼] We consider a simple stochastic model of an urban rental housing market, in which the interaction of tenants and landlords induces rent fluctuations. We simulate the model numerically and measure the equilibrium rent distribution, which is found to be close to a lognormal law. We also study the influence of the density of agents (or equivalently, the vacancy rate) on the rent distribution. A simplified version of the model, amenable to analytical treatment, is studied and leads to a lognormal distribution of rents. The predicted equilibrium value agrees quantitatively with numerical simulations, while a qualitative agreement is obtained for the standard deviation. The connection with non-equilibrium statistical physics models such as ratchets is also emphasized. [less ▲] Detailed reference viewed: 87 (4 UL)Modified fluctuation-dissipation theorem for general non-stationary states and application to the Glauber-Ising chain Verley, Gatien ; ; in Journal of Statistical Mechanics: Theory and Experiment (2011), (10), 10025 In this paper, we present a general derivation of a modified fluctuation-dissipation theorem (MFDT) valid near an arbitrary non-stationary state for a system obeying Markovian dynamics. We show that the ... [more ▼] In this paper, we present a general derivation of a modified fluctuation-dissipation theorem (MFDT) valid near an arbitrary non-stationary state for a system obeying Markovian dynamics. We show that the method for deriving modified fluctuation-dissipation theorems near non-equilibrium stationary states used by Prost et al (2009 Phys. Rev. Lett. 103 090601) is generalizable to non-stationary states. This result follows from both standard linear response theory and from a transient fluctuation theorem, analogous to the Hatano?Sasa relation. We show that this modified fluctuation-dissipation theorem can be interpreted at the trajectory level using the notion of stochastic trajectory entropy in a way which is similar to what has been done recently in the case of the MFDT near non-equilibrium steady states (NESS). We illustrate this framework with two solvable examples: the first example corresponds to a Brownian particle in a harmonic trap subjected to a quench of temperature and to a time-dependent stiffness; the second example is a classic model of coarsening systems, namely the 1D Ising model with Glauber dynamics. [less ▲] Detailed reference viewed: 91 (2 UL)Extracting chemical energy by growing disorder: efficiency at maximum power Esposito, Massimiliano ; ; in Journal of Statistical Mechanics: Theory and Experiment (2010) We consider the efficiency of chemical energy extraction from the environment by the growth of a copolymer made of two constituent units in the entropy-driven regime. We show that the thermodynamic ... [more ▼] We consider the efficiency of chemical energy extraction from the environment by the growth of a copolymer made of two constituent units in the entropy-driven regime. We show that the thermodynamic nonlinearity associated with the information processing aspect is responsible for a branching of the system properties such as power, speed of growth, entropy production, and efficiency, with varying affinity. The standard linear thermodynamics argument which predicts an efficiency of 1/2 at maximum power is inappropriate because the regime of maximum power is located either outside of the linear regime or on a separate bifurcated branch, and because the usual thermodynamic force is not the natural variable for this optimization. [less ▲] Detailed reference viewed: 77 (1 UL)Extracting chemical energy by growing disorder: efficiency at maximum power Esposito, Massimiliano ; ; in Journal of Statistical Mechanics: Theory and Experiment (2010) Detailed reference viewed: 64 (2 UL) |
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