Early Stages of Homopolymer Collapse

Interest in the protein folding problem has motivated a wide range of theoretical and experimental studies of the kinetics of the collapse of flexible homopolymers. In this Paper a phenomenological model is proposed for the kinetics of the early stages of homopolymer collapse following a quench from temperatures above to below the theta temperature. In the first stage, nascent droplets of the dense phase are formed, with little effect on the configurations of the bridges that join them. The droplets then grow by accreting monomers from the bridges, thus causing the bridges to stretch. During these two stages the overall dimensions of the chain decrease only weakly. Further growth of the droplets is accomplished by the shortening of the bridges, which causes the shrinking of the overall dimensions of the chain. The characteristic times of the three stages respectively scale as the zeroth, 1/5 and 6/5 power of the the degree of polymerization of the chain.Comment: 11 pages, 3 figure

Two refreshing views of Fluctuation Theorems through Kinematics Elements and Exponential Martingale

In the context of Markov evolution, we present two original approaches to obtain Generalized Fluctuation-Dissipation Theorems (GFDT), by using the language of stochastic derivatives and by using a family of exponential martingales functionals. We show that GFDT are perturbative versions of relations verified by these exponential martingales. Along the way, we prove GFDT and Fluctuation Relations (FR) for general Markov processes, beyond the usual proof for diffusion and pure jump processes. Finally, we relate the FR to a family of backward and forward exponential martingales.Comment: 41 pages, 7 figures; version2: 45 pages, 7 figures, minor revisions, new results in Section

Quantum Fluctuation Relations for the Lindblad Master Equation

An open quantum system interacting with its environment can be modeled under suitable assumptions as a Markov process, described by a Lindblad master equation. In this work, we derive a general set of fluctuation relations for systems governed by a Lindblad equation. These identities provide quantum versions of Jarzynski-Hatano-Sasa and Crooks relations. In the linear response regime, these fluctuation relations yield a fluctuation-dissipation theorem (FDT) valid for a stationary state arbitrarily far from equilibrium. For a closed system, this FDT reduces to the celebrated Callen-Welton-Kubo formula