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fluctuation theorem for the mutation process in in vitro evolution

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Chinese Physics B 2010年第4期19卷 11-15页

作者：刘琪汤超欧阳颀 Department of Physics Peking University Center for Theoretical Biology Peking University California Institute for Quantitative Biomedical Research Departments of Biopharmaceutical Sciences and Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCA 94143USA

A proposition based on the fluctuation theorem in thermodynamics is formulated to quantitatively describe molecular evolution processes in biology. Although we cannot give full proof of its generality, we demonstrate via computer simulation its applicability in an example of DNA in vitro evolution. According to this theorem, the evolution process is a series of exponentially rare fluctuations fixed by the force of natural selection

关键词： fluctuation theorem molecular evolution natural selection

fluctuation theorem for entropy production in a chemical reaction channel

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Science China Chemistry 2010年第2期53卷 396-401页

作者： XIAO TieJun HOU ZhongHuai Hefei National Laboratory for Physical Sciences at the Microscale Department of Chemical PhysicsUniversity of Science and Technology of ChinaHefei 230026China

fluctuation theorem for entropy production in a mesoscopic chemical reaction network is discussed. When the system size is sufficiently large, it is found that, by defining a kind of coarse-grained dissipation function, the entropy production in a reversible reaction channel can be approximately described by a type of detailed fluctuation theorem. Such a fluctuation relation has been successfully tested by direct simulations in a linear reaction model consisting of two reversible channels and in an oscillatory model wherein only one channel is reversible.

关键词： nonequilibrium thermodynamics chemical reaction network entropy production fluctuation theorem

Nonequilibrium thermodynamics and fluctuation relations for small systems

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Chinese Physics B 2014年第7期23卷 30-40页

作者：曹亮柯谱乔丽颜郑志刚 Department of Physics and the Beijing–Hong Kong–Singapore Joint Center for Nonlinear and Complex Studies Beijing Normal University

In this review, we give a retrospect of the recent progress in nonequilibrium statistical mechanics and thermodynamics in small dynamical systems. For systems with only a few number of particles, fluctuations and nonlinearity become sig- nificant and contribute to the nonequilibrium behaviors of the systems, hence the statistical properties and thermodynamics should be carefully studied. We review recent developments of this topic by starting from the Gallavotti-Cohen fluctuation theorem, and then to the Evans-Searles transient fluctuation theorem, Jarzynski free-energy equality, and the Crooks fluc- tuation relation. We also investigate the nonequilibrium free energy theorem for trajectories involving changes of the heat bath temperature and propose a generalized free-energy relation. It should be noticed that the non-Markovian property of the heat bath may lead to the violation of the free-energy relation.

关键词： free-energy equality fluctuation theorem Markov process detailed balance

Stochastic fluctuations in the rotation of the bacterial flagellar motor

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Chinese Physics B 2023年第6期32卷 106-111页

作者：岳冠骅张榕京袁军华 Department of Physics University of Science and Technology of ChinaHefei 230026China

The bacterial flagellar motor is a nanometer-sized rotary motor that generates the torque to drive the rotation of the flagellar *** output torque is an important property of the *** motor rotation was usually monitored by attaching aμm-sized bead to a shortened flagellar filament,and the torque was extracted by calculating the torque due to the viscous drag of the medium on the bead *** sought for an independent extraction of the torque from thermal fluctuation in the motor rotation using the fluctuation theorem(FT).However,we identified an overwhelming fluctuation beyond the thermal noise that precluded the use of *** further characterized the timescale and the amplitude of this fluctuation,finding that it was probably due to the stepping of the *** amplitude of torque fluctuation we characterized here provided new information on the torque-generating interaction potential curve.

关键词： motor torque bacterial motility fluctuation theorem viscous drag

A Possible Generalized Form of Jarzynski Equality

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Communications in Theoretical Physics 2006年第5X期46卷 886-890页

作者： TU Zhan-Chun ZHOU Zi-Cong Department of Physics Tamkang University Tamsui 25137 Taiwan China Physics Division National Center for Theoretical Sciences at Taipei National Taiwan University Taipei 10617 Taiwan China

The crucial condition in the derivation of the Jarzynski equality （JE） from the fluctuation theorem is that the time integral of the phase space contraction factor can be exactly expressed as the entropy production resulting from the heat absorbed by the system from the thermal bath. For the system violating this condition, a more general form of JE may exist. This existence is verified by three Gedanken experiments and numerical simulations, and may be confirmed by the real experiment in the nanoscale.

关键词： Jarzynski equality fluctuation theorem entropy production

Stochastic Thermodynamics of Mesoscopic Electrochemical Reactions

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Chinese Journal of Chemical Physics 2018年第1期31卷 61-65,I0001页

作者：肖铁军周匀贵州师范学院贵州省纳米材料模拟与计算重点实验室贵州省科学云大数据开发及其产业应用协同创新中心

In this work, we discussed the stochastic thermodynamics of mesoscopic electron transfer reactions between ions and electrodes. With a relationship between the reaction rate con- stant and the electrode potential, we find that the heat dissipation βq equals to the dynamic irreversibility of the reaction system minus an internal entropy change term. The total en- tropy change Ast is defined as the summation of the system entropy change As and the heat dissipation/βq such that △st=△s＋βq. Even though the heat dissipation depends linearly on the electrode potential, the total entropy change is found to satisfy the fluctuation theo- rem 〈e-△st 〉=1, and hence a second law-like inequality reads （△st）≥0. Our study provides a practical methodology for the stochastic thermodynamics of electrochemical reactions, which may find applications in biochemical and electrochemical reaction systems.

关键词： Mesoscopic chemical reaction Electron transfer Electrode potential Entropyproduction fluctuation theorem

The Harmonic Oscillator with Random Damping in Non-Markovian Thermal Bath

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World Journal of Mechanics 2016年第8期6卷 238-248页

作者： N. J. Hassan A. Pourdarvish J. Sadeghi Department of Statistics Faculty of Mathematical Sciences University of Mazandran Babolsar Iran Department of Physics Faculty of Basic Science University of Mazandaran Babolsar Iran

In this paper, we define the harmonic oscillator with random damping in non-Markovian thermal bath. This model represents new version of the random oscillators. In this side, we derive the overdamped harmonic oscillator with multiplicative colored noise and translate it into the additive colored noise by changing the variables. The overdamped harmonic oscillator is stochastic differential equation driving by colored noise. We derive the change in the total entropy production (CTEP) of the model and calculate the mean and variance. We show the fluctuation theorem (FT) which is invalid at any order in the time correlation. The problem of the deriving of the CTEP is studied in two different examples of the harmonic potential. Finally, we give the conclusion and plan for future works.

关键词： Random Damping Total Entropy Non-Markovian Bath fluctuation theorem Additive Colored Noise