1,478 results on '"fluctuation theorem"'
Search Results
52. Information Thermodynamics Derives the Entropy Current of Cell Signal Transduction as a Model of a Binary Coding System.
- Author
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Tsuruyama, Tatsuaki
- Subjects
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CELLULAR signal transduction , *FLUCTUATIONS (Physics) , *MATHEMATICS theorems , *THERMODYNAMICS , *ENTROPY (Information theory) - Abstract
The analysis of cellular signaling cascades based on information thermodynamics has recently developed considerably. A signaling cascade may be considered a binary code system consisting of two types of signaling molecules that carry biological information, phosphorylated active, and non-phosphorylated inactive forms. This study aims to evaluate the signal transduction step in cascades from the viewpoint of changes in mixing entropy. An increase in active forms may induce biological signal transduction through a mixing entropy change, which induces a chemical potential current in the signaling cascade. We applied the fluctuation theorem to calculate the chemical potential current and found that the average entropy production current is independent of the step in the whole cascade. As a result, the entropy current carrying signal transduction is defined by the entropy current mobility. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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53. Entropy Production in Ecosystems
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Virgo, Nathaniel, Harvey, Inman, Carbonell, Jaime G., editor, Siekmann, J\'org, editor, Almeida e Costa, Fernando, editor, Rocha, Luis Mateus, editor, Costa, Ernesto, editor, Harvey, Inman, editor, and Coutinho, António, editor
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- 2007
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54. 4 Maximum Entropy Production and Non-equilibrium Statistical Mechanics
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Dewar, Roderick C., Kleidon, Axel, editor, and Lorenz, Ralph D., editor
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- 2005
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55. Stochastic Dynamics of Proteins and the Action of Biological Molecular Machines
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Michal Kurzynski and Przemyslaw Chelminiak
- Subjects
protein dynamics ,conformational transition networks ,fractal-small world transition ,fluctuation theorem ,biological molecular machines ,free energy transduction ,Science ,Astrophysics ,QB460-466 ,Physics ,QC1-999 - Abstract
It is now well established that most if not all enzymatic proteins display a slow stochastic dynamics of transitions between a variety of conformational substates composing their native state. A hypothesis is stated that the protein conformational transition networks, as just as higher-level biological networks, the protein interaction network, and the metabolic network, have evolved in the process of self-organized criticality. Here, the criticality means that all the three classes of networks are scale-free and, moreover, display a transition from the fractal organization on a small length-scale to the small-world organization on the large length-scale. Good mathematical models of such networks are stochastic critical branching trees extended by long-range shortcuts. Biological molecular machines are proteins that operate under isothermal conditions and hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free energy-donating (input) reaction and the free energy-accepting (output) one. The far-from-equilibrium degree of coupling between the output and the input reaction fluxes have been studied both theoretically and by means of the Monte Carlo simulations on model networks. For single input and output gates the degree of coupling cannot exceed unity. Study simulations of random walks on model networks involving more extended gates indicate that the case of the degree of coupling value higher than one is realized on the mentioned above critical branching trees extended by long-range shortcuts.
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- 2014
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56. Information in Biological Systems and the Fluctuation Theorem
- Author
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Yaşar Demirel
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information theory ,biological systems ,fluctuation theorem ,thermodynamic coupling ,Science ,Astrophysics ,QB460-466 ,Physics ,QC1-999 - Abstract
Some critical trends in information theory, its role in living systems and utilization in fluctuation theory are discussed. The mutual information of thermodynamic coupling is incorporated into the generalized fluctuation theorem by using information theory and nonequilibrium thermodynamics. Thermodynamically coupled dissipative structures in living systems are capable of degrading more energy, and processing complex information through developmental and environmental constraints. The generalized fluctuation theorem can quantify the hysteresis observed in the amount of the irreversible work in nonequilibrium regimes in the presence of information and thermodynamic coupling.
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- 2014
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57. Fitness Gain of Individually Sensed Information by Cells
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Tetsuya J. Kobayashi and Yuki Sughiyama
- Subjects
fluctuation theorem ,evolution ,decision-making ,directed information ,information thermodynamics ,auto-encoder ,Science ,Astrophysics ,QB460-466 ,Physics ,QC1-999 - Abstract
Mutual information and its causal variant, directed information, have been widely used to quantitatively characterize the performance of biological sensing and information transduction. However, once coupled with selection in response to decision-making, the sensing signal could have more or less evolutionary value than its mutual or directed information. In this work, we show that an individually sensed signal always has a better fitness value, on average, than its mutual or directed information. The fitness gain, which satisfies fluctuation relations (FRs), is attributed to the selection of organisms in a population that obtain a better sensing signal by chance. A new quantity, similar to the coarse-grained entropy production in information thermodynamics, is introduced to quantify the total fitness gain from individual sensing, which also satisfies FRs. Using this quantity, the optimizing fitness gain of individual sensing is shown to be related to fidelity allocations for individual environmental histories. Our results are supplemented by numerical verifications of FRs, and a discussion on how this problem is linked to information encoding and decoding.
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- 2019
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58. Fluctuation Theorem of Information Exchange within an Ensemble of Paths Conditioned on Correlated-Microstates
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Lee Jinwoo
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local non-equilibrium thermodynamics ,fluctuation theorem ,mutual information ,entropy production ,local mutual information ,thermodynamics of information ,stochastic thermodynamics ,Science ,Astrophysics ,QB460-466 ,Physics ,QC1-999 - Abstract
Fluctuation theorems are a class of equalities that express universal properties of the probability distribution of a fluctuating path functional such as heat, work or entropy production over an ensemble of trajectories during a non-equilibrium process with a well-defined initial distribution. Jinwoo and Tanaka (Jinwoo, L.; Tanaka, H. Sci. Rep. 2015, 5, 7832) have shown that work fluctuation theorems hold even within an ensemble of paths to each state, making it clear that entropy and free energy of each microstate encode heat and work, respectively, within the conditioned set. Here we show that information that is characterized by the point-wise mutual information for each correlated state between two subsystems in a heat bath encodes the entropy production of the subsystems and heat bath during a coupling process. To this end, we extend the fluctuation theorem of information exchange (Sagawa, T.; Ueda, M. Phys. Rev. Lett. 2012, 109, 180602) by showing that the fluctuation theorem holds even within an ensemble of paths that reach a correlated state during dynamic co-evolution of two subsystems.
- Published
- 2019
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59. Fluctuation Theorem of Information Exchange between Subsystems that Co-Evolve in Time
- Author
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Lee Jinwoo
- Subjects
fluctuation theorem ,thermodynamics of information ,stochastic thermodynamics ,mutual information ,non-equilibrium free energy ,entropy production ,Mathematics ,QA1-939 - Abstract
Sagawa and Ueda established a fluctuation theorem of information exchange by revealing the role of correlations in stochastic thermodynamics and unified the non-equilibrium thermodynamics of measurement and feedback control. They considered a process where a non-equilibrium system exchanges information with other degrees of freedom such as an observer or a feedback controller. They proved the fluctuation theorem of information exchange under the assumption that the state of the other degrees of freedom that exchange information with the system does not change over time while the states of the system evolve in time. Here we relax this constraint and prove that the same form of the fluctuation theorem holds even if both subsystems co-evolve during information exchange processes. This result may extend the applicability of the fluctuation theorem of information exchange to a broader class of non-equilibrium processes, such as a dynamic coupling in biological systems, where subsystems that exchange information interact with each other.
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- 2019
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60. Quantum measurement arrow of time and fluctuation relations for measuring spin of ultracold atoms
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Nicholas P. Bigelow, Sreenath K. Manikandan, Andrew N. Jordan, and Maitreyi Jayaseelan
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Physics ,Condensed Matter::Quantum Gases ,Multidisciplinary ,Quantum information ,Fluctuation theorem ,Science ,General Physics and Astronomy ,General Chemistry ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Article ,010305 fluids & plasmas ,Ultracold atom ,Arrow of time ,Quantum mechanics ,0103 physical sciences ,Weak measurement ,Statistical physics ,Physics::Atomic Physics ,010306 general physics ,Spin (physics) ,Quantum thermodynamics ,Wave function collapse ,Quantum - Abstract
The origin of macroscopic irreversibility from microscopically time-reversible dynamical laws—often called the arrow-of-time problem—is of fundamental interest in both science and philosophy. Experimentally probing such questions in quantum theory requires systems with near-perfect isolation from the environment and long coherence times. Ultracold atoms are uniquely suited to this task. We experimentally demonstrate a striking parallel between the statistical irreversibility of wavefunction collapse and the arrow of time problem in the weak measurement of the quantum spin of an atomic cloud. Our experiments include statistically rare events where the arrow of time is inferred backward; nevertheless we provide evidence for absolute irreversibility and a strictly positive average arrow of time for the measurement process, captured by a fluctuation theorem. We further demonstrate absolute irreversibility for measurements performed on a quantum many-body entangled wavefunction—a unique opportunity afforded by our platform—with implications for studying quantum many-body dynamics and quantum thermodynamics., Irreversibility in quantum measurements shares conceptual links with statistical and thermodynamical irreversibility. Here, the authors are able to operationally associate an "arrow of time” to quantum weak measurements, testing it experimentally on a cloud of ultracold atoms.
- Published
- 2021
61. Some Recent Advances in Classical Statistical Mechanics
- Author
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Cohen, E. G. D., Beig, R., editor, Englert, B. -G., editor, Frisch, U., editor, Hänggi, P., editor, Hepp, K., editor, Hillebrandt, W., editor, Imboden, D., editor, Jaffe, R. L., editor, Lipowsky, R., editor, v. Löhneysen, H., editor, Ojima, I., editor, Sornette, D., editor, Theisen, S., editor, Weise, W., editor, Wess, J., editor, Zittartz, J., editor, Garbaczewski, Piotr, editor, and Olkiewicz, Robert, editor
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- 2002
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62. Thermohaline circulation: a missing equation and its climate-change implications.
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Ou, Hsien-Wang
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MERIDIONAL overturning circulation , *CLIMATE change , *GLOBAL warming , *GENERAL circulation model , *MAXIMUM entropy method - Abstract
We formulate a box model of coupled ocean-atmosphere to examine the differential fields interactive with the thermohaline circulation (THC) and their response to global warming. We discern a robust convective bound on the atmospheric heat transport, which would divide the climate regime into warm and cold branches; but unlike the saline mode of previous box models, the cold state, if allowed, has the same-signed-though weaker-density contrast and THC as the present climate, which may explain its emergence from coupled general circulation models. We underscore the nondeterminacy of the THC due to random eddy shedding and apply the fluctuation theorem to constrain the shedding rate, thus closing the problem. The derivation reveals an ocean propelled toward the maximum entropy production (MEP) on millennial timescale (termed 'MEP-adjustment'), the long timescale arising from the compounding effect of microscopic fluctuations in the shedding rate and their slight probability bias. Global warming may induce hysteresis between the two branches, like that seen in GCMs, but the cold transition is far more sensitive to the moistening than the heating effects as the latter would be countered by the hydrological feedback. The uni- or bi-modality of the current state-hence whether the THC may recover after the cold transition-depends on the global-mean convective flux and may not be easily assessed due to its observed uncertainty. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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63. 増殖•進化適応系に内在する情報熱力学的構造.
- Author
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小林徹也 and 杉山友規
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NATURAL selection , *PHENOTYPES , *ENTROPY , *BIOLOGICAL adaptation , *BIOLOGICAL evolution - Abstract
The adaptability to ever-changing environment is one of the fundamental characteristics that differentiates living matters from non-living ones. The combination of passive adaptation by Darwinian evolution and active adaptation by sensing and decision-making shapes the mechanisms of adaptability. In this work, we outline that the biological adaptation shares a very similar structure with the stochastic and information-thermodynamics. Fitness, the macroscopic quantity to characterize evolutionary success, plays the similar role as the free energy in this structure. The fluctuation relation of fitness and information derived from the structure can be regarded as an extension of the concept of the evolutionary stable strategy. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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64. Role of work in matter exchange between finite quantum systems.
- Author
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Euijin Jeon, Talkner, Peter, Juyeon Yi, and Yong Woon Kim
- Subjects
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QUANTUM mechanics , *EQUILIBRIUM , *CHEMICAL potential , *MACROSCOPIC cross sections , *HEAT exchangers - Abstract
Close to equilibrium, the exchange of particles and heat between macroscopic systems at different temperatures and different chemical potentials is known to be governed by a matrix of transport coefficients which are positive and symmetric. We investigate the amounts of heat and particles that are exchanged between two small quantum systems within a given time, and find them characterized by a transport matrix which neither needs to be symmetric nor positive. At larger times even spontaneous transport can be observed in the total absence of temperature and chemical potential differences provided that the two systems are different in size. All these deviations from standard transport behavior can be attributed to the fact that work is done on the system in the processes contacting and separating those parts of the system that initially possess different temperatures and chemical potentials. The standard transport properties are recovered for vanishing work and also in the limit of large systems and sufficiently large contact times. The general results are illustrated by an example. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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65. Rotational Brownian Motion: Trajectory, Reversibility and Stochastic Entropy.
- Author
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Bandopadhyay, Swarnali, Chaudhuri, Debasish, and Jayannavar, A.
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WIENER processes , *STOCHASTIC processes , *ENTROPY , *DISTRIBUTION (Probability theory) , *COMPUTER simulation - Abstract
Stochastic motion of macrospins is similar to driven diffusion of Brownian particles on the surface of a sphere. One crucial difference is in how the micro-states transform under time reversal. This dictates the form of stochastic entropy production (sEP). An excess sEP in the reservoir, in addition to a Clausius term, may appear depending on the interpretation of stochastic trajectory, thereby, precluding such analysis without a detailed knowledge of the governing dynamics. To show this, we derive expressions of sEP using Fokker-Planck equation, and the ratio of probability distributions of time-forward and time-reversed trajectories. We calculate probability distributions of sEP using numerical simulations, and obtain good agreement with the detailed fluctuation theorem. Within adiabatic approximation, analytic form for the distribution function is also derived. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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66. Fluctuation theorem of a mesoscopic engine and spin switching.
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Utsumi, Yasuhiro and Taniguchi, Tomohito
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FLUCTUATIONS (Physics) , *MESOSCOPIC systems , *STOCHASTIC processes , *THRESHOLD voltage , *MAGNETIC moments , *FLUCTUATION-dissipation relationships (Physics) - Abstract
Based on the fluctuation theorem of a small engine, we present a description of the stochastic dynamics of a mesoscopic system. We apply it to the problem of the escape of a particle from a metastable state subjected to a fluctuating nonconservative force, which is beyond the description of the fluctuation-dissipation theorem. As an example, we consider a reversal of a small magnetic moment by fluctuating spin-torque. The joint probability distribution of input heat and output work is derived from the full-counting statistics under adiabatic pumping. We predict a threshold voltage above which the spin-torque shot noise induces probabilistic switching events, and below which such events are blocked. [ABSTRACT FROM AUTHOR]
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- 2017
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67. Steady-state distributions of probability fluxes on complex networks.
- Author
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Chełminiak, Przemysław and Kurzyński, Michał
- Subjects
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DISTRIBUTION (Probability theory) , *MARKOV processes , *COMPUTER simulation , *GAUSSIAN distribution , *NONLINEAR theories , *PARAMETERS (Statistics) - Abstract
We consider a simple model of the Markovian stochastic dynamics on complex networks to examine the statistical properties of the probability fluxes. The additional transition, called hereafter a gate, powered by the external constant force breaks a detailed balance in the network. We argue, using a theoretical approach and numerical simulations, that the stationary distributions of the probability fluxes emergent under such conditions converge to the Gaussian distribution. By virtue of the stationary fluctuation theorem, its standard deviation depends directly on the square root of the mean flux. In turn, the nonlinear relation between the mean flux and the external force, which provides the key result of the present study, allows us to calculate the two parameters that entirely characterize the Gaussian distribution of the probability fluxes both close to as well as far from the equilibrium state. Also, the other effects that modify these parameters, such as the addition of shortcuts to the tree-like network, the extension and configuration of the gate and a change in the network size studied by means of computer simulations are widely discussed in terms of the rigorous theoretical predictions. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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68. Random walks on quasi one dimensional lattices: Large deviations and fluctuation theorems.
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Faggionato, Alessandra and Silvestri, Vittoria
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RANDOM walks , *DISCRETE probability theory , *LATTICE theory , *LARGE deviations (Mathematics) , *MARKOV random fields - Abstract
Several stochastic processes modeling molecular motors on a linear track are given by random walks (not necessarily Markovian) on quasi 1d lattices and share a common regenerative structure. Analyzing this abstract common structure, we derive information on the large fluctuations of the stochastic process by proving large deviation principles for the first-passage times and for the position.We focus our attention on the Gallavotti-Cohen-type symmetry of the position rate function (fluctuation theorem), showing its equivalence with the independence of suitable random variables. In the special case of Markov random walks, we show that this symmetry is universal only inside a suitable class of quasi 1d lattices. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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69. Admitting Spontaneous Violations of the Second Law in Continuum Thermomechanics.
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Ostoja-Starzewski, Martin
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CONTINUUM mechanics , *ELASTICITY , *ENTROPY , *STOCHASTIC analysis , *THERMOMECHANICAL treatment - Abstract
We survey new extensions of continuum mechanics incorporating spontaneous violations of the Second Law (SL), which involve the viscous flow and heat conduction. First, following an account of the Fluctuation Theorem (FT) of statistical mechanics that generalizes the SL, the irreversible entropy is shown to evolve as a submartingale. Next, a stochastic thermomechanics is formulated consistent with the FT, which, according to a revision of classical axioms of continuum mechanics, must be set up on random fields. This development leads to a reformulation of thermoviscous fluids and inelastic solids. These two unconventional constitutive behaviors may jointly occur in nano-poromechanics. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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70. Entropy Balance, Multibaker Maps, and the Dynamics of the Lorentz Gas
- Author
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Tél, T., Vollmer, J., Fröhlich, J., editor, Novikov, S. P., editor, Ruelle, D., editor, Bunimovich, L. A., Burago, D., Chernov, N., Cohen, E. G. D., Dettmann, C. P., Dorfman, J. R., Ferleger, S., Hirschl, R., Kononenko, A., Lebowitz, J. L., Liverani, C., Murphy, T. J., Piasecki, J., Posch, H. A., Simányi, N., Sinai, Ya., Szász, D., Tél, T., van Beijeren, H., van Zon, R., Vollmer, J., and Young, L. S.
- Published
- 2000
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71. Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics
- Author
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Christoph Dellago and Gerhard Hummer
- Subjects
fast switching simulations ,non-equilibrium work theorem ,fluctuation theorem ,non-equilibrium molecular dynamics ,Science ,Astrophysics ,QB460-466 ,Physics ,QC1-999 - Abstract
As shown by Jarzynski, free energy differences between equilibrium states can be expressed in terms of the statistics of work carried out on a system during non-equilibrium transformations. This exact result, as well as the related Crooks fluctuation theorem, provide the basis for the computation of free energy differences from fast switching molecular dynamics simulations, in which an external parameter is changed at a finite rate, driving the system away from equilibrium. In this article, we first briefly review the Jarzynski identity and the Crooks fluctuation theorem and then survey various algorithms building on these relations. We pay particular attention to the statistical efficiency of these methods and discuss practical issues arising in their implementation and the analysis of the results.
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- 2013
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72. Hierarchical Information Entropy System Model for TWfMS
- Author
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Qiang Han and Deren Yang
- Subjects
Trustworthy Workflow Management System ,information entropy system model ,fluctuation theorem ,dissipative structure system ,the second law of thermodynamics ,system engineering ,service computing ,software engineering ,Science ,Astrophysics ,QB460-466 ,Physics ,QC1-999 - Abstract
Under the infrastructure of three gradually deepening layers consisting of System, Service and Software, the information entropy of the Trustworthy Workflow Management System (TWfMS) will evolve from being more precise to more undetermined, due to a series of exception event X occurring on certain components (ExCs), along with the life cycle of TWfMS, experienced in its phased original, as-is, to-be, and agile-consistent stages, and recover, more precisely again, by turning back to the original state from the agile-consistent stage, due to its self-autonomous improvement. With a special emphasis on the system layer, to assure the trustworthiness of WfMS, this paper firstly introduces the preliminary knowledge of the hierarchical information entropy model with correlation theories. After illustrating the fundamental principle, the transformation rule is deduced, step by step, followed by a case study, which is conducive to generating discussions and conclusions in the different research areas of TWfMS. Overall, in this paper, we argue that the trustworthiness maintenance of WfMS could be analyzed and computational, through the viewpoint that all the various states of TWfMS can be considered as the transformation between WfMS and its trustworthiness compensate components, whose information entropy fluctuate repeatedly and comply with the law of the dissipative structure system.
- Published
- 2018
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73. Entropy in Cell Biology: Information Thermodynamics of a Binary Code and Szilard Engine Chain Model of Signal Transduction
- Author
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Tatsuaki Tsuruyama
- Subjects
biological reaction cascade ,binary code system ,average entropy production rate ,mutual entropy ,Szilard engine chain ,fluctuation theorem ,Science ,Astrophysics ,QB460-466 ,Physics ,QC1-999 - Abstract
A model of signal transduction from the perspective of informational thermodynamics has been reported in recent studies, and several important achievements have been obtained. The first achievement is that signal transduction can be modelled as a binary code system, in which two forms of signalling molecules are utilised in individual steps. The second is that the average entropy production rate is consistent during the signal transduction cascade when the signal event number is maximised in the model. The third is that a Szilard engine can be a single-step model in the signal transduction. This article reviews these achievements and further introduces a new chain of Szilard engines as a biological reaction cascade (BRC) model. In conclusion, the presented model provides a way of computing the channel capacity of a BRC.
- Published
- 2018
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74. Detailed Fluctuation Theorems: A Unifying Perspective
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Riccardo Rao and Massimiliano Esposito
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stochastic thermodynamics ,fluctuation theorem ,Markov jump process ,entropy production ,graph theory ,conservation laws ,Science ,Astrophysics ,QB460-466 ,Physics ,QC1-999 - Abstract
We present a general method to identify an arbitrary number of fluctuating quantities which satisfy a detailed fluctuation theorem for all times within the framework of time-inhomogeneous Markovian jump processes. In doing so, we provide a unified perspective on many fluctuation theorems derived in the literature. By complementing the stochastic dynamics with a thermodynamic structure (i.e., using stochastic thermodynamics), we also express these fluctuating quantities in terms of physical observables.
- Published
- 2018
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75. Analysis of Cell Signal Transduction Based on Kullback–Leibler Divergence: Channel Capacity and Conservation of Its Production Rate during Cascade
- Author
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Tatsuaki Tsuruyama
- Subjects
average entropy production rate ,fluctuation theorem ,signal transduction ,Science ,Astrophysics ,QB460-466 ,Physics ,QC1-999 - Abstract
Kullback–Leibler divergence (KLD) is a type of extended mutual entropy, which is used as a measure of information gain when transferring from a prior distribution to a posterior distribution. In this study, KLD is applied to the thermodynamic analysis of cell signal transduction cascade and serves an alternative to mutual entropy. When KLD is minimized, the divergence is given by the ratio of the prior selection probability of the signaling molecule to the posterior selection probability. Moreover, the information gain during the entire channel is shown to be adequately described by average KLD production rate. Thus, this approach provides a framework for the quantitative analysis of signal transduction. Moreover, the proposed approach can identify an effective cascade for a signaling network.
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- 2018
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76. The Conservation of Average Entropy Production Rate in a Model of Signal Transduction: Information Thermodynamics Based on the Fluctuation Theorem
- Author
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Tatsuaki Tsuruyama
- Subjects
signal transduction ,fluctuation theorem ,average entropy production rate ,Science ,Astrophysics ,QB460-466 ,Physics ,QC1-999 - Abstract
Cell signal transduction is a non-equilibrium process characterized by the reaction cascade. This study aims to quantify and compare signal transduction cascades using a model of signal transduction. The signal duration was found to be linked to step-by-step transition probability, which was determined using information theory. By applying the fluctuation theorem for reversible signal steps, the transition probability was described using the average entropy production rate. Specifically, when the signal event number during the cascade was maximized, the average entropy production rate was found to be conserved during the entire cascade. This approach provides a quantitative means of analyzing signal transduction and identifies an effective cascade for a signaling network.
- Published
- 2018
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77. Information Thermodynamics of the Cell Signal Transduction as a Szilard Engine
- Author
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Tatsuaki Tsuruyama
- Subjects
Szilard engine ,mutual entropy ,signal transduction ,information thermodynamics ,fluctuation theorem ,Science ,Astrophysics ,QB460-466 ,Physics ,QC1-999 - Abstract
A cell signaling system is in a non-equilibrium state, and it includes multistep biochemical signaling cascades (BSCs), which involve phosphorylation of signaling molecules, such as mitogen-activated protein kinase (MAPK) pathways. In this study, the author considered signal transduction description using information thermodynamic theory. The ideal BSCs can be considered one type of the Szilard engine, and the presumed feedback controller, Maxwell’s demon, can extract the work during signal transduction. In this model, the mutual entropy and chemical potential of the signal molecules can be redefined by the extracted chemical work in a mechanicochemical model, Szilard engine, of BSC. In conclusion, signal transduction is computable using the information thermodynamic method.
- Published
- 2018
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78. Linear Response and Correlation Functions
- Author
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Risken, Hannes, Haken, Hermann, editor, and Risken, Hannes
- Published
- 1996
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79. Quantum–Classical Correspondence Principle for Heat Distribution in Quantum Brownian Motion
- Author
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Haitao Quan, Jin-Fu Chen, and Tian Qiu
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Work (thermodynamics) ,heat statistics ,Science ,QC1-999 ,General Physics and Astronomy ,FOS: Physical sciences ,Astrophysics ,Classical limit ,Article ,open quantum systems ,phase-space formulation ,quantum Brownian motion ,Phase space formulation ,Quantum thermodynamics ,Brownian motion ,Condensed Matter - Statistical Mechanics ,Physics ,Quantum Physics ,Statistical Mechanics (cond-mat.stat-mech) ,Fluctuation theorem ,Langevin equation ,QB460-466 ,Classical mechanics ,Correspondence principle ,Quantum Physics (quant-ph) - Abstract
Quantum Brownian motion, described by the Caldeira-Leggett model, brings insights to understand phenomena and essence of quantum thermodynamics, especially the quantum work and heat associated with their classical counterparts. By employing the phase-space formulation approach, we study the heat distribution of a relaxation process in the quantum Brownian motion model. The analytical result of the characteristic function of heat is obtained at any relaxation time with an arbitrary friction coefficient. By taking the classical limit, such a result approaches the heat distribution of the classical Brownian motion described by the Langevin equation, indicating the quantum-classical correspondence principle for heat distribution. We also demonstrate that the fluctuating heat at any relaxation time satisfies the exchange fluctuation theorem of heat, and its long-time limit reflects complete thermalization of the system. Our research brings justification for the definition of the quantum fluctuating heat via two-point measurements., Comment: 32 pages, 2 figures
- Published
- 2021
80. Quantum Thermodynamics with Degenerate Eigenstate Coherences.
- Author
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Cuetara, Gregory Bulnes, Esposito, Massimiliano, and Schaller, Gernot
- Subjects
- *
QUANTUM thermodynamics , *QUANTUM coherence , *QUANTUM dots , *DEGENERATE perturbation theory , *FLUCTUATIONS (Physics) - Abstract
We establish quantum thermodynamics for open quantum systems weakly coupled to their reservoirs when the system exhibits degeneracies. The first and second law of thermodynamics are derived, as well as a finite-time fluctuation theorem for mechanical work and energy and matter currents. Using a double quantum dot junction model, local eigenbasis coherences are shown to play a crucial role on thermodynamics and on the electron counting statistics. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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81. Synchronization and fluctuation theorems for interacting Friedman urns.
- Author
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Sahasrabudhe, Neeraja
- Subjects
FRACTIONAL calculus ,FRIEDMAN test (Statistics) ,SYNCHRONIZATION ,FLUCTUATIONS (Physics) ,LIMIT theorems - Abstract
We consider a model of N interacting two-colour Friedman urns. The interaction model considered is such that the reinforcement of each urn depends on the fraction of balls of a particular colour in that urn as well as the overall fraction of balls of that colour in all the urns combined together. We show that the urns synchronize almost surely and that the fraction of balls of each colour converges to the deterministic limit of one-half, which matches with the limit known for a single Friedman urn. Furthermore, we use the notion of stable convergence to obtain limit theorems for fluctuations around the synchronization limit. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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82. Fluctuations of Linear Eigenvalues Statistics for Wigner Matrices: Edge Case.
- Author
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Pan, Guangming, Wang, Shaochen, and Zhou, Wang
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WIGNER rotation matrix , *EIGENVALUES , *HERMITIAN forms , *GAUSSIAN distribution , *STATISTICS , *LINEAR statistical models - Abstract
In this note, we consider the fluctuation theorem for $$X_{f_n}^{(n)}:=\sum _{i=1}^n f(\lambda _i)I(\lambda _i\ge \theta _n)$$ , where $$\lambda _i, i=1,\ldots ,n$$ are eigenvalues from a Wigner matrix and $$\theta _n\rightarrow 2^-$$ . We prove that in the edge case $$X_{f_n}^{(n)}$$ behaves like the counting function of Wigner matrix. Our results can be viewed as a complement of Bao et al. (J Stat Phys 150(1):88-129, 2013). [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
83. Continuum mechanics versus violations of the second law of thermodynamics.
- Author
-
Ostoja-Starzewski, Martin and Venkatesh Raghavan, Bharath
- Subjects
- *
CONTINUUM mechanics , *ANALYTICAL mechanics , *FIELD theory (Physics) , *QUANTUM theory , *HEAT engines - Abstract
Spontaneous, random violations of the second law become relevant as the length and/or timescales become very small. Modern statistical physics tells us that the second law then needs to be replaced by the fluctuation theorem and, mathematically, the irreversible entropy evolves as a submartingale. This is illustrated on the Couette flow of a molecular fluid. On the continuum level, such phenomena lead to a framework of thermomechanics relying on stochastic (rather than deterministic) functionals of energy and entropy, which are applied in heat diffusion and thermoelasticity settings. Counterintuitive thermomechanical behaviors are also discussed in (1) the evolution of acceleration wavefronts of nanoscale thickness and (2) the fluid mechanics which has to enter a permeability model of a poroelastic medium with nanoscale pores. [ABSTRACT FROM PUBLISHER]
- Published
- 2016
- Full Text
- View/download PDF
84. The mechanism of inward rectification in Kir channels: A novel kinetic model with non-equilibrium thermodynamics approach.
- Author
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Hsieh, Chi-Pan, Chiang, Cheng-Chin, and Huang, Chiung-Wei
- Subjects
- *
POTASSIUM channels , *RECTIFICATION (Electrophysiology) , *NONEQUILIBRIUM thermodynamics , *ELECTRIC potential , *POTASSIUM antagonists , *CHEMICAL kinetics - Abstract
The mechanisms of the strong inward rectification in inward rectifier K + (Kir) channels are controversial because the drop in electrical potential due to the movement of the blocker and coupling ions is insufficient to explain the steep voltage-dependent block near the equilibrium potential. Here, we study the “driving force”-dependent block in Kir channels with a novel approach incorporating concepts from the non-equilibrium thermodynamics of small systems, and computer kinetic simulations based on the experimental data of internal Ba 2 + block on Kir2.1 channels. The steep exponential increase in the apparent binding rate near the equilibrium potential is explained, when the encounter frequency is construed as the likelihood of transfer events down or against the electrochemical potential gradient. The exponent of flux ratio, n f = 2.62, implies that the blockage of the internal blocker may be coupled with the outward transport of 2 to 3 K + ions. The flux-coupled block in the single-file multi-ion pore can be demonstrated by the concentration gradient alone, as well as when the driving force is the electrochemical potential difference across the membrane. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
85. Mechanism for asymmetric bias in demonstrations of the NPI and fluctuation theorem.
- Author
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Petersen, Charlotte F., Evans, Denis J., and Williams, Stephen R.
- Subjects
- *
FLUCTUATIONS (Physics) , *PARTITION coefficient (Chemistry) , *NON-equilibrium reactions , *APPROXIMATION theory , *LINEAR statistical models - Abstract
We consider two different methods of calculating the relevant average for the non-equilibrium partition identity (NPI), i.e., which result in two different values. At best only one of these will accurately correspond to what is observed. In order to better understand the two outcomes we carry out a detailed error analysis. This analysis is difficult due to the importance of extremely rare events in forming the average, resulting in the necessity to go beyond linear approximations for the error estimates. We begin by analysing the error in the fluctuation relation, and build upon this to estimate the errors in the NPI average. At short durations the full ensemble average always gives the observed average (i.e. the NPI holds). However, at very long durations, given a fixed amount of sampling, the observed average is predicted by treating the probability distribution as a Dirac-delta function. At intermediate times, neither corresponds to the observed average. This has profound implications for non-equilibrium work relations, as first introduced by Jarzynski. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
86. Second law violations, continuum mechanics, and permeability.
- Author
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Ostoja-Starzewski, Martin
- Subjects
- *
CONTINUUM mechanics , *PERMEABILITY , *FLUCTUATIONS (Physics) , *MATHEMATICS theorems , *MICROPOLAR elasticity - Abstract
The violations of the second law are relevant as the length and/or time scales become very small. The second law then needs to be replaced by the fluctuation theorem and mathematically, the irreversible entropy is a submartingale. First, we discuss the consequences of these results for the axioms of continuum mechanics, arguing in favor of a framework relying on stochastic functionals of energy and entropy. We next determine a Lyapunov function for diffusion-type problems governed by stochastic rather than deterministic functionals of internal energy and entropy, where the random field coefficients of diffusion are not required to satisfy the positive definiteness everywhere. Next, a formulation of micropolar fluid mechanics is developed, accounting for the lack of symmetry of stress tensor on molecular scales. This framework is then applied to employed to show that spontaneous random fluctuations of the microrotation field will arise in Couette-and Poiseuille-type flows in the absence of random (turbulence-like) fluctuations of the classical velocity field. Finally, while the permeability is classically modeled by the Darcy law or its modifications, besides considering the violations of the second law, one also needs to account for the spatial randomness of the channel network, implying a modification of the hierarchy of scale-dependent bounds on the macroscopic property of the network. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
87. Fluctuation theorems for synchronization of interacting Pólya’s urns.
- Author
-
Crimaldi, Irene, Dai Pra, Paolo, and Minelli, Ida Germana
- Subjects
- *
FLUCTUATIONS (Physics) , *SYNCHRONIZATION , *PARAMETER estimation , *STOCHASTIC convergence , *DISTRIBUTION (Probability theory) - Abstract
We consider a system of N two-colors urns in which the reinforcement of each urn depends also on the content of all the other urns. This interaction is of mean-field type and it is tuned by a parameter α ∈ [ 0 , 1 ] ; in particular, for α = 0 the N urns behave as N independent Pólya’s urns. For α > 0 urns synchronize, in the sense that the fraction of balls of a given color converges a.s. to the same (random) limit in all urns. In this paper we study fluctuations around this synchronized regime. The scaling of these fluctuations depends on the parameter α . In particular the standard scaling t − 1 / 2 appears only for α > 1 / 2 . For α ≥ 1 / 2 we also determine the limit distribution of the rescaled fluctuations. We use the notion of stable convergence, which is stronger than convergence in distribution. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
88. Steps toward the foundations of statistical mechanics: in and out of equilibrium
- Author
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D.Karevski
- Subjects
foundations of statistical mechanics ,fluctuation theorem ,jarzynski equality ,Physics ,QC1-999 - Abstract
The first part of the paper is devoted to the foundations, that is the mathematical and physical justification, of equilibrium statistical mechanics. It is a pedagogical attempt, mostly based on Khinchin's presentation, which purpose is to clarify some aspects of the development of statistical mechanics. In the second part, we discuss some recent developments that appeared out of equilibrium, such as fluctuation theorem and Jarzynski equality.
- Published
- 2006
- Full Text
- View/download PDF
89. Entropy production of a closed Hamiltonian system via the detailed fluctuation relation
- Author
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Masahito Ueda, Naoto Kura, and Yûto Murashita
- Subjects
Nonlinear Sciences::Chaotic Dynamics ,Physics ,Relation (database) ,Entropy production ,Fluctuation theorem ,Statistical physics ,Imperfect ,Hamiltonian system - Abstract
We revisit the problem of emergent irreversibility in a closed Hamiltonian system in light of the detailed fluctuation relation by invoking an imperfect Loschmidt demon that performs a time-reversal operation with a finite precision. The imperfect time reversal can be utilized to evaluate entropy production \`a la Kolmogorov and Sinai in a manner consistent with the fluctuation theorem with absolute irreversibility.
- Published
- 2021
- Full Text
- View/download PDF
90. Conservation laws shape dissipation
- Author
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Riccardo Rao and Massimiliano Esposito
- Subjects
stochastic thermodynamics ,network ,fluctuation theorem ,conservation law ,entropy production ,cycles ,Science ,Physics ,QC1-999 - Abstract
Starting from the most general formulation of stochastic thermodynamics—i.e. a thermodynamically consistent nonautonomous stochastic dynamics describing systems in contact with several reservoirs—we define a procedure to identify the conservative and the minimal set of nonconservative contributions in the entropy production. The former is expressed as the difference between changes caused by time-dependent drivings and a generalized potential difference. The latter is a sum over the minimal set of flux-force contributions controlling the dissipative flows across the system. When the system is initially prepared at equilibrium (e.g. by turning off drivings and forces), a finite-time detailed fluctuation theorem holds for the different contributions. Our approach relies on identifying the complete set of conserved quantities and can be viewed as the extension of the theory of generalized Gibbs ensembles to nonequilibrium situations.
- Published
- 2018
- Full Text
- View/download PDF
91. Stochastic thermodynamics and hierarchy of fluctuation theorems with multiple reservoirs
- Author
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Jae Sung Lee and Hyunggyu Park
- Subjects
stochastic thermodynamics ,fluctuation theorem ,multiple reservoir ,noise-mixing ,Science ,Physics ,QC1-999 - Abstract
We reformulate stochastic thermodynamics in terms of noise realizations for Langevin systems in contact with multiple reservoirs and investigate the structure of the second laws of thermodynamics. We derive a hierarchy of fluctuation theorems when one degree of freedom of the system is affected by multiple reservoirs simultaneously, that is, when noise-mixing occurs. These theorems and the associated second laws of thermodynamics put stricter bounds on the thermodynamics of Langevin systems. We apply our results to a stochastic machine in noise-mixing environments and demonstrate that our new bounds play a crucial role in determining the potential function and performance of the machine.
- Published
- 2018
- Full Text
- View/download PDF
92. On fluctuating momentum exchange in idealised models of air–sea interaction
- Author
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Achim Wirth, Laboratoire des Écoulements Géophysiques et Industriels [Grenoble] (LEGI ), and Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
- Subjects
[SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere ,Cultural Studies ,Physics ,010504 meteorology & atmospheric sciences ,Fluctuation theorem ,lcsh:QC801-809 ,Momentum transfer ,Atmospheric motion ,Random forcing ,01 natural sciences ,lcsh:QC1-999 ,010305 fluids & plasmas ,Education ,lcsh:Geophysics. Cosmic physics ,Stochastic differential equation ,Phase space ,0103 physical sciences ,lcsh:Q ,[PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Fluid mechanics [physics.class-ph] ,Statistical physics ,lcsh:Science ,lcsh:Physics ,Physics::Atmospheric and Oceanic Physics ,0105 earth and related environmental sciences - Abstract
International audience; The dynamics of three local models, for momentum transfer at the air-sea interface, is compared. The models differ by whether or not the ocean velocity is included in the shear calculation applied to the ocean and the atmosphere. All three cases are employed in climate or ocean simulations. Analytic calculations for the models with deterministic and random forcing (white and coloured) are presented. The short term behaviour is similar in all models, which only small quantitative differences, while the long-term behaviour differs qualitatively between the models. The fluctuation-dissipation-relation, which 5 connects the fast atmospheric motion to the slow oceanic dynamics, is established for all models with random forcing. The fluctuation-dissipation-theorem, which compares the response to an external forcing to internal fluctuations is established for a white-noise forcing and a coloured forcing when the phase space is augmented by the forcing variable. Using results from numerical integrations of stochastic differential equations it is shown that the fluctuation-theorem, which compares the probability of positive to negative fluxes of the same magnitude, averaged over time-intervals of varying length, holds for the 10 energy gained by the ocean from the atmosphere.
- Published
- 2019
- Full Text
- View/download PDF
93. Investigation of multiple-dynein transport of melanosomes by non-invasive force measurement using fluctuation unit χ
- Author
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Yasushi Okada, Shin Hasegawa, Kazuho Ikeda, Kumiko Hayashi, and Takashi Sagawa
- Subjects
0301 basic medicine ,Dynein ,Melanophores ,Kinesins ,lcsh:Medicine ,macromolecular substances ,Microtubules ,Article ,Melanophore ,03 medical and health sciences ,0302 clinical medicine ,Microtubule ,Organelle ,Animals ,lcsh:Science ,Zebrafish ,Quinazolinones ,Melanosome ,Organelles ,Physics ,Melanosomes ,Multidisciplinary ,biology ,Fluctuation theorem ,lcsh:R ,Dyneins ,biology.organism_classification ,030104 developmental biology ,Biophysics ,Kinesin ,Drosophila ,lcsh:Q ,030217 neurology & neurosurgery - Abstract
Pigment organelles known as melanosomes disperse or aggregate in a melanophore in response to hormones. These movements are mediated by the microtubule motors kinesin-2 and cytoplasmic dynein. However, the force generation mechanism of dynein, unlike that of kinesin, is not well understood. In this study, to address this issue, we investigated the dynein-mediated aggregation of melanosomes in zebrafish melanophores. We applied the fluctuation theorem of non-equilibrium statistical mechanics to estimate forces acting on melanosomes during transport by dynein, given that the energy of a system is related to its fluctuation. Our results demonstrate that multiple force-producing units cooperatively transport a single melanosome. Since the force is generated by dynein, this suggests that multiple dyneins carry a single melanosome. Cooperative transport has been reported for other organelles; thus, multiple-motor transport may be a universal mechanism for moving organelles within the cell.
- Published
- 2019
- Full Text
- View/download PDF
94. A Theoretical Analysis of the Integral Fluctuation Theorem for Accelerated Colloidal Systems in the Long-Time Limit
- Author
-
Yash Lokare
- Subjects
Physics ,Colloid ,Fluctuation theorem ,Quantum electrodynamics ,Time limit ,acoustics - Abstract
A quantitative description of the second law of thermodynamics in relatively small classical systems and over short time scales comes from the fluctuation-dissipation theorem. It has been well established both theoretically and experimentally, the validity of the fluctuation theorem to small scale systems that are disturbed from their initial equilibrium states. Some experimental studies in the past have also explored the validity of the fluctuation theorem to nonequilibrium steady states at long time scales in the asymptotic limit. To this end, a theoretical and/or purely numerical model of the integral fluctuation theorem has been presented. An approximate general expression for the dissipation function has been derived for accelerated colloidal systems trapped/confined in power-law traps. Thereafter, a colloidal particle trapped in a harmonic potential (generated by an accelerating one-dimensional optical trap) and undergoing Brownian motion has been considered for the numerical study. A toy model of a quartic potential trap in addition to the harmonic trap has also been considered for the numerical study. The results presented herein show that the integral fluctuation theorem applies not only to equilibrium steady state distributions but also to nonequilibrium steady state distributions of ideal colloidal systems in accelerated frames of reference over long time scales.
- Published
- 2021
95. Finite-time fluctuation theorem for oscillatory lattices driven by a temperature gradient
- Author
-
Dahai He and Jinhong Li
- Subjects
Physics ,Entropy production ,Fluctuation theorem ,Anharmonicity ,Non-equilibrium thermodynamics ,Monotonic function ,01 natural sciences ,Symmetry (physics) ,010305 fluids & plasmas ,Entropy (classical thermodynamics) ,Distribution (mathematics) ,0103 physical sciences ,Statistical physics ,010306 general physics - Abstract
The finite-time fluctuation theorem (FT) for the master functional, total entropy production, and medium entropy is studied in the one-dimensional Fermi-Pasta-Ulam-Tsingou-β (FPUT-β) chain coupled with two heat reservoirs at different temperatures. Through numerical simulations and theoretical analysis, we find that the nonequilibrium steady-state distribution of the one-dimensional FPUT-β chain violates the time-reversal symmetry. Thus, unlike the master functional, the total entropy production fails to satisfy the fluctuation relation for finite time. Meanwhile, we discuss the range of medium entropy production which obeys the conventional steady-state fluctuation theorem (SSFT) in the infinite time limit. Furthermore, we find that the generalized SSFT for medium entropy monotonically approaches the conventional SSFT as the time interval increases, irrespective of temperature difference, anharmonicity, and system size. Interestingly, the medium entropy production rate shows a nonmonotonic variation with anharomonicity, which comes from a competition mechanism of the phonon transport. Correspondingly, the difference between the generalized SSFT and the conventional SSFT shows similar nonmonotonic behaviors.
- Published
- 2021
- Full Text
- View/download PDF
96. On the analysis of the integral fluctuation theorem for accelerated colloidal systems in the long-time limit
- Author
-
Yash Lokare
- Subjects
Physics ,Toy model ,Steady state ,Fluctuation theorem ,Quartic function ,media_common.quotation_subject ,Non-equilibrium thermodynamics ,Second law of thermodynamics ,Statistical physics ,Dissipation ,Brownian motion ,media_common - Abstract
A quantitative description of the violation of the second law of thermodynamics in relatively small classical systems and over short time scales comes from the fluctuation-dissipation theorem. It has been well established both theoretically and experimentally, the validity of the fluctuation theorem to small scale systems that are disturbed from their initial equilibrium states. Some experimental studies in the past have also explored the validity of the fluctuation theorem to nonequilibrium steady states at long time scales in the asymptotic limit. To this end, a theoretical and/or purely numerical model of the integral fluctuation theorem has been presented. An approximate general expression for the dissipation function has been derived for accelerated colloidal systems trapped/confined in power-law traps. Thereafter, a colloidal particle trapped in a harmonic potential (generated by an accelerating one-dimensional optical trap) and undergoing Brownian motion has been considered for the numerical study. A toy model of a quartic potential trap in addition to the harmonic trap has also been considered for the numerical study. The results presented herein show that the integral fluctuation theorem applies not only to equilibrium steady state distributions but also to nonequilibrium steady state distributions of colloidal systems in accelerated frames of reference over long time scales.
- Published
- 2021
- Full Text
- View/download PDF
97. Fluctuation theorems from Bayesian retrodiction
- Author
-
Valerio Scarani and Francesco Buscemi
- Subjects
Quantum Physics ,Statistical Mechanics (cond-mat.stat-mech) ,Fluctuation theorem ,Bayesian probability ,FOS: Physical sciences ,Non-equilibrium thermodynamics ,Statistical mechanics ,01 natural sciences ,Object (philosophy) ,010305 fluids & plasmas ,Mechanical system ,0103 physical sciences ,Retrodiction ,Statistical physics ,Quantum Physics (quant-ph) ,010306 general physics ,Quantum ,Condensed Matter - Statistical Mechanics ,Mathematics - Abstract
Quantitative studies of irreversibility in statistical mechanics often involve the consideration of a reverse process, whose definition has been the object of many discussions, in particular for quantum mechanical systems. Here we show that the reverse channel very naturally arises from Bayesian retrodiction, both in classical and quantum theories. Previous paradigmatic results, such as Jarzynski's equality, Crooks' fluctuation theorem, and Tasaki's two-measurement fluctuation theorem for closed driven quantum systems, are all shown to be consistent with retrodictive arguments. Also, various corrections that were introduced to deal with nonequilibrium steady states or open quantum systems are justified on general grounds as remnants of Bayesian retrodiction. More generally, with the reverse process constructed on consistent logical inference, fluctuation relations acquire a much broader form and scope., v4: greatly expanded and with new examples, accepted for publication on PRE; v3: various improvements in the presentation and examples added (fluctuation relations for f-divergences); v2: discussion expanded, refs added, now a little more than 5 two-column pages; v1:5 two-column pages
- Published
- 2021
- Full Text
- View/download PDF
98. Thermodynamics of inequalities: From precariousness to economic stratification.
- Author
-
Smerlak, Matteo
- Subjects
- *
THERMODYNAMICS , *ECONOMIC development , *ECONOPHYSICS , *MARKOV processes , *MATHEMATICAL inequalities , *ENTROPY - Abstract
Growing economic inequalities are observed in several countries throughout the world. Following Pareto, the power-law structure of these inequalities has been the subject of much theoretical and empirical work. But their nonequilibrium dynamics , e.g. after a policy change, remains incompletely understood. Here we introduce a thermodynamical theory of inequalities based on the analogy between economic stratification and statistical entropy. Within this framework we identify the combination of upward mobility with precariousness as a fundamental driver of inequality. We formalize this statement by a “second-law” inequality displaying upward mobility and precariousness as thermodynamic conjugate variables. We estimate the time scale for the “relaxation” of the wealth distribution after a sudden change of the after-tax return on capital. Our method can be generalized to gain insight into the dynamics of inequalities in any Markovian model of socioeconomic interactions. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
99. Model for bidirectional movement of cytoplasmic dynein.
- Author
-
Sumathy, S. and Satyanarayana, S.V.M.
- Subjects
- *
CYTOPLASM , *DYNEIN , *ADENOSINE triphosphate , *MONTE Carlo method , *VELOCITY - Abstract
Cytoplasmic dynein exhibits a directional processive movement on microtubule filaments and is known to move in steps of varying length based on the number of ATP molecules bound to it and the load that it carries. It is experimentally observed that dynein takes occasional backward steps and the frequency of such backward steps increases as the load approaches the stall force. Using a stochastic process model, we investigate the bidirectional movement of single head of a dynein motor. The probability for backward step is implemented based on fluctuation theorem of non-equilibrium statistical mechanics. We find that the movement of dynein motor is characterized with negative velocity implying backward motion beyond stall force. We observe that the motor moves backward for super stall forces by hydrolyzing the ATP exactly the same way as it does while moving forward for sub-stall forces. Movement of dynein is also simulated using a kinetic Monte Carlo method and the simulated velocities are in good agreement with velocities obtained using a stochastic rate equation model. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
100. Direct Observation of the Reversible Two-State Unfolding and Refolding of an α/β Protein by Single-Molecule Atomic Force Microscopy.
- Author
-
He, Chengzhi, Hu, Chunguang, Hu, Xiaodong, Hu, Xiaotang, Xiao, Adam, Perkins, Thomas T., and Li, Hongbin
- Subjects
- *
ATOMIC force microscopy , *PROTEIN folding , *CHEMICAL equilibrium , *CHEMICAL reactions , *CHEMICAL stability - Abstract
Directly observing protein folding in real time using atomic force microscopy (AFM) is challenging. Here the use of AFM to directly monitor the folding of an α/β protein, NuG2, by using low-drift AFM cantilevers is demonstrated. At slow pulling speeds (<50 nm s−1), the refolding of NuG2 can be clearly observed. Lowering the pulling speed reduces the difference between the unfolding and refolding forces, bringing the non-equilibrium unfolding-refolding reactions towards equilibrium. At very low pulling speeds (ca. 2 nm s−1), unfolding and refolding were observed to occur in near equilibrium. Based on the Crooks fluctuation theorem, we then measured the equilibrium free energy change between folded and unfolded states of NuG2. The improved long-term stability of AFM achieved using gold-free cantilevers allows folding-unfolding reactions of α/β proteins to be directly monitored near equilibrium, opening the avenue towards probing the folding reactions of other mechanically important α/β and all-β elastomeric proteins. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
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