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Stochastic mechanochemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist's perspective
 Physics ReportsReview Section of Physics Letters
, 2013
"... A molecular motor is made of either a single macromolecule or a macromolecular complex. Just like their macroscopic counterparts, molecular motors “transduce ” input energy into mechanical work. All the nanomotors considered here operate under isothermal conditions far from equilibrium. Moreover, ..."
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A molecular motor is made of either a single macromolecule or a macromolecular complex. Just like their macroscopic counterparts, molecular motors “transduce ” input energy into mechanical work. All the nanomotors considered here operate under isothermal conditions far from equilibrium. Moreover, one of the possible mechanisms of energy transduction, called Brownian ratchet, does not even have any macroscopic counterpart. But, molecular motor is not synonymous with Brownian ratchet; a large number of molecular motors execute a noisy power stroke, rather than operating as Brownian ratchet. We review not only the structural design and stochastic kinetics of individual single motors, but also their coordination, cooperation and competition as well as the assembly of multimodule motors in various intracellular kinetic processes. Although all the motors considered here execute mechanical movements, efficiency and power output are not necessarily good measures of performance of some motors. Among the intracellular nanomotors, we consider the porters, sliders and rowers, pistons and hooks, exporters, importers, packers and movers as well as those that also synthesize, manipulate and degrade “macromolecules of life”. We review mostly the quantitative models for the kinetics of these motors. We also describe several of those motordriven intracellular stochastic processes for which quantitative models are yet to be developed. In part I, we discuss mainly the methodology and the generic models of various important classes of molecular motors. In part II, we review many specific examples emphasizing the unity of the basic mechanisms as well as diversity of operations arising from the differences in their detailed structure and kinetics. Multidisciplinary research is presented here from the perspective of physicists.
FactChecking Ziegler’s Maximum Entropy Production Principle beyond the Linear Regime and towards Steady States
 ENTROPY
, 2013
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A Theory of Mesoscopic Phenomena: Time scales, emergent
, 2013
"... unpredictability, symmetry breaking and dynamics across different levels ..."
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unpredictability, symmetry breaking and dynamics across different levels
Thermal Contact I. Symmetries ruled by Exchange Entropy Variations
, 2013
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The zeroth law of thermodynamics and volumepreserving conservative system in equilibrium with stochastic damping
 Phys. Lett. A
, 2014
"... We propose a mathematical formulation of the zeroth law of thermodynamics and develop a stochastic dynamical theory, with a consistent irreversible thermodynamics, for systems possessing sustained conservative stationary current in phase space while in equilibrium with a heat bath. The theory gene ..."
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We propose a mathematical formulation of the zeroth law of thermodynamics and develop a stochastic dynamical theory, with a consistent irreversible thermodynamics, for systems possessing sustained conservative stationary current in phase space while in equilibrium with a heat bath. The theory generalizes underdamped mechanical equilibrium: dx = gdt + {−D∇φdt + √2DdB(t)}, with ∇ · g = 0 and { · · · } respectively representing phasevolume preserving dynamics and stochastic damping. The zeroth law implies stationary distribution uss(x) = e−φ(x). We find an orthogonality ∇φ · g = 0 as a hallmark of the system. Stochastic thermodynamics based on time reversal t, φ, g) → ( − t, φ,−g) is formulated: entropy production e#p (t) = −dF (t)/dt; generalized “heat” h#d (t) = −dU(t)/dt, U(t) = Rn φ(x)u(x, t)dx being “internal energy”, and “free energy” F (t) = U(t)+ Rn u(x, t) lnu(x, t)dx never increases. Entropy follows dS dt = e#p −h#d. Our formulation is shown to be consistent with an earlier theory of P. Ao. Its contradistinctions to other theories, potentialflux decomposition, stochastic Hamiltonian system with even and odd variables, KleinKramers equation, FreidlinWentzell’s theory, and GENERIC, are discussed.
Azabicyclo[2.1.1]hexanes. A review
 Heterocycles
, 2004
"... doi: 10.3389/fpls.2012.00261 The impact of genome triplication on tandem gene evolution in Brassica rapa Lu Fang†, Feng Cheng, JianWu and XiaowuWang* ..."
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doi: 10.3389/fpls.2012.00261 The impact of genome triplication on tandem gene evolution in Brassica rapa Lu Fang†, Feng Cheng, JianWu and XiaowuWang*
Determining the Statistics of Fluctuating Currents: General Markovian Dynamics and its Application to Motor Proteins
, 2014
"... Fluctuations in biological systems are commonly modeled by Markovian jump processes. Here we present a method for the analytical calculation of the fluctuation spectrum for any fluctuating physical current – without need to solve for the steadystate probability distribution. Our result provides a g ..."
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Fluctuations in biological systems are commonly modeled by Markovian jump processes. Here we present a method for the analytical calculation of the fluctuation spectrum for any fluctuating physical current – without need to solve for the steadystate probability distribution. Our result provides a generalization of the Schnakenberg decomposition for currents to their fluctuation spectrum at arbitrary order. The decomposition shows that topological cycles in the system fully characterize the steadystate statistics. For the biochemical motor protein kinesin our method reproduces previous results via considerably less involved calculations, and it unveils previously hidden features of the models.
OF DICE AND MEN. SUBJECTIVE PRIORS, GAUGE INVARIANCE, AND NONEQUILIBRIUM THERMODYNAMICS
"... “Ceci n’est pas une pipe ” wrote Rene ́ Magritte on what was only the representation of a pipe. Phenomena and their physical descriptions differ, and in particular the laws ruling the former might enjoy symmetries that have to be spent to attain the latter. So, inertial frames are necessary to draw ..."
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“Ceci n’est pas une pipe ” wrote Rene ́ Magritte on what was only the representation of a pipe. Phenomena and their physical descriptions differ, and in particular the laws ruling the former might enjoy symmetries that have to be spent to attain the latter. So, inertial frames are necessary to draw numbers out of Newtonian mechanics and confront with experiment, but ultimately the laws of mechanics are independent of reference frames. Generalizing work done in Ref. [M. Polettini, EPL 97 (2012) 30003] to continuous systems, we discuss from a foundational point of view how subjectivity in the choice of reference prior probability is a (gauge) symmetry of thermodynamics. In particular, a change of priors corresponds to a change of coordinates. Employing an approach based on the stochastic thermodynamics of continuous statespace diffusion processes, we discuss the difference between thermostatic and thermodynamic observables and show that, while the quantification of entropy depends on priors, the second law of thermodynamics is formulated in terms of invariant quantities, in particular the curvature of the thermodynamic force (gauge potential), which we calculate in a few examples of processes led by different nonequilibrium mechanisms.
The Harmonic Oscillator with Random Damping in NonMarkovian Thermal Bath
"... Abstract In this paper, we define the harmonic oscillator with random damping in nonMarkovian 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 c ..."
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Abstract In this paper, we define the harmonic oscillator with random damping in nonMarkovian 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.