Entropy Production of Nanosystems with Time Scale Separation

Wang, Shou-Wen; Kawaguchi, Kyogo; Sasa, Shin Ichi; Tang, Lei-Han

doi:10.1103/physrevlett.117.070601

Cited by 42 publications

(48 citation statements)

References 36 publications

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“…With this approach, it was shown how the entropy production obtained from the mesoscopic dynamics, gives a lower bound on the total rate of entropy production. Interestingly, in systems characterized by a large separation of timescales [205] where only the slow variables are monitored, the hidden entropy production arising from the coupling between slow and fast degrees of freedom, can be recovered using Eq. (13).…”

Section: Entropy Production and Stochastic Thermodynamicsmentioning

confidence: 99%

Broken detailed balance and non-equilibrium dynamics in living systems: a review

et al. 2018

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Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as high-fidelity transcription and translation, sensing, adaptation, biochemical patterning, and force generation. While biological systems such as motor enzymes violate detailed balance at the molecular scale, it remains unclear how non-equilibrium dynamics manifests at the mesoscale in systems that are driven through the collective activity of many motors. Indeed, in several cellular systems the presence of non-equilibrium dynamics is not always evident at large scales. For example, in the cytoskeleton or in chromosomes one can observe stationary stochastic processes that appear at first glance thermally driven. This raises the question how non-equilibrium fluctuations can be discerned from thermal noise. We discuss approaches that have recently been developed to address this question, including methods based on measuring the extent to which the system violates the fluctuation-dissipation theorem. We also review applications of this approach to reconstituted cytoskeletal networks, the cytoplasm of living cells, and cell membranes. Furthermore, we discuss a more recent approach to detect actively driven dynamics, which is based on inferring broken detailed balance. This constitutes a non-invasive method that uses time-lapse microscopy data, and can be applied to a broad range of systems in cells and tissue. We discuss the ideas underlying this method and its application to several examples including flagella, primary cilia, and cytoskeletal networks. Finally, we briefly discuss recent developments in stochastic thermodynamics and non-equilibrium statistical mechanics, which offer new perspectives to understand the physics of living systems.

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Section: Entropy Production and Stochastic Thermodynamicsmentioning

confidence: 99%

Broken detailed balance and non-equilibrium dynamics in living systems: a review

et al. 2018

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“…The authors of Ref. [42] showed that systems subject to fast drivings display a violation of the fluctuationresponse relation and evaluated its typical shape in the space of frequencies for large time-scale separations. Such violation of the fluctuation response relation is known to be linked to entropy production for Langevin systems by the Harada-Sasa equality [93].…”

Section: Entropy For Block-diagonal Dynamicsmentioning

confidence: 99%

Multiple-scale stochastic processes: Decimation, averaging and beyond

Bò

Celani

2017

Physics Reports

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The recent experimental progresses in handling microscopic systems have allowed to probe them at levels where fluctuations are prominent, calling for stochastic modeling in a large number of physical, chemical and biological phenomena. This has provided fruitful applications for established stochastic methods and motivated further developments. These systems often involve processes taking place on widely separated time scales. For an efficient modeling one usually focuses on the slower degrees of freedom and it is of great importance to accurately eliminate the fast variables in a controlled fashion, carefully accounting for their net effect on the slower dynamics. This procedure in general requires to perform two different operations: decimation and coarse-graining. We introduce the asymptotic methods that form the basis of this procedure and discuss their application to a series of physical, biological and chemical examples. We then turn our attention to functionals of the stochastic trajectories such as residence times, counting statistics, fluxes, entropy production, etc. which have been increasingly studied in recent years. For such functionals, the elimination of the fast degrees of freedom can present additional difficulties and naive procedures can lead to blatantly inconsistent results. Homogenization techniques for functionals are less covered in the literature and we will pedagogically present them here, as natural extensions of the ones employed for the trajectories. We will also discuss recent applications of these techniques to the thermodynamics of small systems and their interpretation in terms of information-theoretic concepts.

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“…Without loss of generality, we set the stationary activity a j u to zero. The activity response function R a is a property of the intracellular molecular network, which can be computed for specific models 38,39 or measured directly in single-cell experiments 3,4,19,40 . In general, R a may depend on the ambient signal level s of the cell.…”

Section: Resultsmentioning

confidence: 99%

“…1 typically follows a dissipative dynamics such as Equation (1). When the medium is close to thermal equilibrium, the Fluctuation-Dissipation Theorem (FDT) relates the imaginary componentR s of the signal responseR s to its spontaneous fluctuationC s induced by thermal noise 38,39,47 : 2TR s (ω) = ωC s (ω), whereC s (ω) = |s(ω)| 2 u is the spectral amplitude of the signal, and T is the temperature. This relation de-mandsR s (ω) to be positive at all frequencies.…”

Section: Resultsmentioning

confidence: 99%

Emergence of collective oscillations in adaptive cells

Wang

Tang

2018

Preprint

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Collective oscillations of cells in a population appear under diverse biological contexts. Here, we establish a set of common principles by categorising the response of individual cells against a timevarying signal. A positive intracellular signal relay of sufficient gain from participating cells is required to sustain the oscillations, together with phase matching. The two conditions yield quantitative predictions for the onset cell density and frequency in terms of measured single-cell and signal response functions. Through mathematical constructions, we show that cells that adapt to a constant stimulus fulfil the phase requirement by developing a leading phase in an active frequency window that enables cell-to-signal energy flow. Analysis of dynamical quorum sensing in several cellular systems with increasing biological complexity reaffirms the pivotal role of adaptation in powering oscillations in an otherwise dissipative cell-to-cell communication channel. The physical conditions identified also apply to synthetic oscillatory systems.

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Entropy Production of Nanosystems with Time Scale Separation

Cited by 42 publications

References 36 publications

Broken detailed balance and non-equilibrium dynamics in living systems: a review

Broken detailed balance and non-equilibrium dynamics in living systems: a review

Multiple-scale stochastic processes: Decimation, averaging and beyond

Emergence of collective oscillations in adaptive cells

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