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      Dynamics and energetics of a molecular zipper under external driving

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          Abstract

          We investigate the dynamics of a single-ended N-state molecular zipper based on a model originally proposed by Kittel. The molecule is driven unidirectionally towards the completely unzipped state with increasing time t, where the driving lowers the energies of states with k unzipped links by an amount proportional to kt. We solve the Pauli rate equation for the state probabilities and the partial differential equations, which yield the probability distributions for the work performed on the zipper and for the heat exchanged with the thermal reservoir. Similarly to the related equilibrium model, two different regimes can be identified at a given temperature with respect to the released molecular degrees of freedom per broken bond. In these two regimes the time evolution of the state probabilities as well as of the work and heat distributions show a qualitatively different behavior.

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          A nonequilibrium equality for free energy differences

          An expression is derived for the classical free energy difference between two configurations of a system, in terms of an ensemble of finite-time measurements of the work performed in parametrically switching from one configuration to the other. Two well-known equilibrium identities emerge as limiting cases of this result.
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            Pulling Pinned Polymers and Unzipping DNA

            We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random DNA sequences with short-ranged correlations, we obtain exact results for the number of monomers liberated and the specific heat, including the critical behavior at the transition. Related systems include a random heteropolymer pulled away from an adsorbing surface and a vortex line in a type II superconductor tilted away from a fragmented columnar defect.
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              The Three Faces of the Second Law: II. Fokker-Planck Formulation

              The total entropy production is the sum of two contributions, the so-called adiabatic and nonadiabatic entropy production, each of which is non-negative. We derive their explicit expressions for continuous Markov processes, discuss their properties and illustrate their behavior on two exactly solvable models.
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                Author and article information

                Journal
                29 March 2012
                2012-10-20
                Article
                10.1088/1742-5468/2012/11/P11009
                1203.6463
                a0ece0c5-4e7f-4366-8811-e301625e1cd5

                http://arxiv.org/licenses/nonexclusive-distrib/1.0/

                History
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                Viktor Holubec et al J. Stat. Mech. (2012) P11009
                18 pages, 6 figures
                cond-mat.stat-mech

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