Nonequilibrium Fluctuations in Small Systems: From Physics to Biology

Ritort, Fèlix

doi:10.1002/9780470238080.ch2

Cited by 181 publications

(221 citation statements)

References 197 publications

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“…We illustrate our results using Carnot cycles based on an overdamped particle diffusing in an externally controlled confining potential. Due to the recent advances in micromanipulation techniques [57], such engines were already realized experimentally [46,58] and hence are of vital theoretical interest [15,42,43,[59][60][61]. The paper is organized as follows.…”

Section: Introductionmentioning

confidence: 99%

Efficiency at and near maximum power of low-dissipation heat engines

Holubec

Ryabov

2015

Phys. Rev. E

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A new universality in optimization of trade-off between power and efficiency for low-dissipation Carnot cycles is presented. It is shown that any trade-off measure expressible in terms of efficiency and the ratio of power to its maximum value can be optimized independently of most details of the dynamics and of the coupling to thermal reservoirs. The result is demonstrated on two specific trade-off measures. The first one is designed for finding optimal efficiency for a given output power and clearly reveals diseconomy of engines working at maximum power. As the second example we derive universal lower and upper bounds on the efficiency at maximum trade-off given by the product of power and efficiency. The results are illustrated on a model of a diffusion-based heat engine. Such engines operate in the low-dissipation regime given that the used driving minimizes the work dissipated during the isothermal branches. The peculiarities of the corresponding optimization procedure are reviewed and thoroughly discussed.

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Section: Introductionmentioning

confidence: 99%

Efficiency at and near maximum power of low-dissipation heat engines

Holubec

Ryabov

2015

Phys. Rev. E

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“…Improvements in measurement devices and techniques; an increasing interest in smaller scale systems in biology, physics, and chemistry [6][7][8][9][10][11]; and developments in dynamical systems and chaos theory [12] have prompted numerous researchers to develop interpretations and extensions of thermodynamics applicable to systems with small numbers of degrees of freedom [8,[13][14][15][16][17]. In such systems it is not possible to uphold the standard interpretation of the thermodynamic quantities and of their relations.…”

Section: Introductionmentioning

confidence: 99%

Phase transition in the Jarzynski estimator of free energy differences

2012

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The transition between a regime in which thermodynamic relations apply only to ensembles of small systems coupled to a large environment and a regime in which they can be used to characterize individual macroscopic systems is analyzed in terms of the change in behavior of the Jarzynski estimator of equilibrium free energy differences from nonequilibrium work measurements. Given a fixed number of measurements, the Jarzynski estimator is unbiased for sufficiently small systems. In these systems the directionality of time is poorly defined and the configurations that dominate the empirical average, but which are in fact typical of the reverse process, are sufficiently well sampled. As the system size increases the arrow of time becomes better defined. The dominant atypical fluctuations become rare and eventually cannot be sampled with the limited resources that are available. Asymptotically, only typical work values are measured. The Jarzynski estimator becomes maximally biased and approaches the exponential of minus the average work, which is the result that is expected from standard macroscopic thermodynamics. In the proper scaling limit, this regime change has been recently described in terms of a phase transition in variants of the random energy model. In this paper this correspondence is further demonstrated in two examples of physical interest: the sudden compression of an ideal gas and adiabatic quasistatic volume changes in a dilute real gas.

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“…Although work is irreversibly dissipated in such measurements, the equilibrium free energy can be reconstructed from the distribution of the non-equilibrium work using fluctuation theorems such as the Jarzynski equality 4 or the Crooks fluctuation theorem 22 . These methods have been tested through nanomechanical measurements of unfolding transitions in single RNA hairpins 7,23 and applied widely 24 . Based on an extension of the Jarzynski equality, Hummer and Szabo proposed an approach to reconstructing the free-energy landscape from non-equilibrium force-ramp measurements 3 .…”

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Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements

et al. 2011

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Free-energy-landscape formalisms provide the fundamental conceptual framework for physical descriptions of how proteins and nucleic acids fold into specific three-dimensional structures 1,2 . Although folding landscapes are difficult to measure experimentally, recent theoretical work by Hummer and Szabo 3 has shown that landscape profiles can be reconstructed from non-equilibrium single-molecule force spectroscopy measurements using an extension of the Jarzynski equality 4 . This method has been applied to simulations 5,6 and experiments 7,8 but never validated experimentally. We tested it using force-extension measurements on DNA hairpins with distinct, sequence-dependent folding landscapes. Quantitative agreement was found between the landscape profiles obtained from the non-equilibrium reconstruction and those from equilibrium probability distributions 9 . We also tested the method on a riboswitch aptamer with three partially folded intermediate states, successfully reconstructing the landscape but finding some states difficult to resolve owing to low occupancy or overlap of the potential wells. These measurements validate the landscape-reconstruction method and provide a new test of non-equilibrium work relations.Folding-landscape formalisms have broad applications in biophysics, from improving predictive structural models and protein engineering 10,11 to providing crucial insights into biomolecular structure, dynamics, function and disease 12,13 . Specific characteristics of folding landscapes, such as the roughness of the free-energy surface 14 or the properties of partially folded intermediate 15 and transition states 16 , including how they are altered by temperature changes, solvent substitutions or mutations 17 , have been widely studied by experiment and theory. However, it has proven remarkably challenging to go beyond such isolated features and measure the entire profile of the free-energy landscape along the reaction coordinate.Single-molecule force spectroscopy provides a unique window into folding reactions because of its ability to measure properties of the free-energy landscape. In single-molecule force spectroscopy, a single molecule is held under mechanical tension by a spring-like force probe such as an optical trap or atomic force microscope, and the end-to-end extension of the molecule is recorded while the molecule folds/unfolds under the influence of the denaturing force (Fig. 1a). By this means, the folding energies and rates, partially folded intermediates and similar characteristics may be explored 18 . Measurements can be made either in the equilibrium regime (for example, by maintaining a constant force using an active 19 1 Department of Physics, University of Alberta, 11322-89 Ave, Edmonton AB, T6G 2G7, Canada, 2 National Institute for Nanotechnology, 11421 Saskatchewan Dr, Edmonton AB, T6G 2M9, Canada. † These authors contributed equally to this work. *e-mail: Michael.woodside@nrc-cnrc.gc.ca. or passive 20 force clamp) or in the non-equilibrium regime (for example, by ramping the ...

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Nonequilibrium Fluctuations in Small Systems: From Physics to Biology

Cited by 181 publications

References 197 publications

Efficiency at and near maximum power of low-dissipation heat engines

Efficiency at and near maximum power of low-dissipation heat engines

Phase transition in the Jarzynski estimator of free energy differences

Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements

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