Out-of-equilibrium versus dynamical and thermodynamical transitions for a model protein

Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a work fluctuation relation, the system free energy landscape is evaluated. Three different structural transitions are identified along the unfolding pathways. Furthermore, the reconstruction of the the free and potential energy profiles in terms of inherent structure formalism allows us to put in direct correspondence these transitions with the equilibrium thermal transitions relevant for protein folding/unfolding. Through the study of the fluctuations of the protein structure at different temperatures, we identify the dynamical transitions, related to configurational rearrangements of the protein, which are precursors of the thermal transitions.Comment: Proceedings of the "YKIS 2009 : Frontiers in Nonequilibrium Physics" conference in Kyoto, August 2009. To appear in Progress of Theoretical Physics Supplemen

Heat flow in chains driven by thermal noise

We consider the large deviation function for a classical harmonic chain composed of N particles driven at the end points by heat reservoirs, first derived in the quantum regime by Saito and Dhar and in the classical regime by Saito and Dhar and Kundu et al. Within a Langevin description we perform this calculation on the basis of a standard path integral calculation in Fourier space. The cumulant generating function yielding the large deviation function is given in terms of a transmission Green's function and is consistent with the fluctuation theorem. We find a simple expression for the tails of the heat distribution which turn out to decay exponentially. We, moreover, consider an extension of a single particle model suggested by Derrida and Brunet and discuss the two-particle case. We also discuss the limit for large N and present a closed expression for the cumulant generating function. Finally, we present a derivation of the fluctuation theorem on the basis of a Fokker-Planck description. This result is not restricted to the harmonic case but is valid for a general interaction potential between the particles.Comment: Latex: 26 pages and 9 figures, appeared in J. Stat. Mech. P04005 (2012

Stationary and transient Fluctuation Theorems for effective heat flux between hydrodynamically coupled particles in optical traps

We experimentally study the statistical properties of the energy fluxes between two trapped Brownian particles, interacting through dissipative hydrodynamic coupling, submitted to an effective temperature difference $\Delta T$, obtained by random forcing the position of one trap. We identify effective heat fluxes between the two particles and show that they satisfy an exchange fluctuation theorem (xFT) in the stationary state. We also show that after the sudden application of a temperature gradient $\Delta T$, \resub{the total} hot-cold flux satisfies \resub{a} transient xFT for any integration time whereas \resub{the total} cold-hot flux only does it asymptotically for long times

Influence of rotational force fields on the determination of the work done on a driven Brownian particle

For a Brownian system the evolution of thermodynamic quantities is a stochastic process. In particular, the work performed on a driven colloidal particle held in an optical trap changes for each realization of the experimental manipulation, even though the manipulation protocol remains unchanged. Nevertheless, the work distribution is governed by established laws. Here, we show how the measurement of the work distribution is influenced by the presence of rotational, i.e. nonconservative, radiation forces. Experiments on particles of different materials show that the rotational radiation forces, and therefore their effect on the work distributions, increase with the particle refractive index.Comment: 12 pages, 4 figure

Fluctuation relations for a driven Brownian particle

We consider a driven Brownian particle, subject to both conservative and non-conservative applied forces, whose probability evolves according to the Kramers equation. We derive a general fluctuation relation, expressing the ratio of the probability of a given Brownian path in phase space with that of the time-reversed path, in terms of the entropy flux to the heat reservoir. This fluctuation relation implies those of Seifert, Jarzynski and Gallavotti-Cohen in different special cases

Fluctuation theorems for harmonic oscillators

We study experimentally the thermal fluctuations of energy input and dissipation in a harmonic oscillator driven out of equilibrium, and search for Fluctuation Relations. We study transient evolution from the equilibrium state, together with non equilibrium steady states. Fluctuations Relations are obtained experimentally for both the work and the heat, for the stationary and transient evolutions. A Stationary State Fluctuation Theorem is verified for the two time prescriptions of the torque. But a Transient Fluctuation Theorem is satisfied for the work given to the system but not for the heat dissipated by the system in the case of linear forcing. Experimental observations on the statistical and dynamical properties of the fluctuation of the angle, we derive analytical expressions for the probability density function of the work and the heat. We obtain for the first time an analytic expression of the probability density function of the heat. Agreement between experiments and our modeling is excellent

Heat distribution function for motion in a general potential at low temperature

We consider the 1D motion of an overdamped Brownian particle in a general potential in the low temperature limit. We derive an explicit expression for the probability distribution for the heat transferred to the particle. We find that the local minima in the potential yield divergent side bands in the heat distribution in addition to the divergent central peak. The position of the bands are determined by the potential gaps. We, moreover, determine the tails of the heat distribution.Comment: 11 pages (latex) and 3 figures (eps

Probability density functions of work and heat near the stochastic resonance of a colloidal particle

We study experimentally and theoretically the probability density functions of the injected and dissipated energy in a system of a colloidal particle trapped in a double well potential periodically modulated by an external perturbation. The work done by the external force and the dissipated energy are measured close to the stochastic resonance where the injected power is maximum. We show a good agreement between the probability density functions exactly computed from a Langevin dynamics and the measured ones. The probability density function of the work done on the particle satisfies the fluctuation theorem

Surface tension in bilayer membranes with fixed projected area

We study the elastic response of bilayer membranes with fixed projected area to both stretching and shape deformations. A surface tension is associated to each of these deformations. By using model amphiphilic membranes and computer simulations, we are able to observe both the types of deformation, and thus, both the surface tensions, related to each type of deformation, are measured for the same system. These surface tensions are found to assume different values in the same bilayer membrane: in particular they vanish for different values of the projected area. We introduce a simple theory which relates the two quantities and successfully apply it to the data obtained with computer simulations

A minimal model of an autonomous thermal motor

We consider a model of a Brownian motor composed of two coupled overdamped degrees of freedom moving in periodic potentials and driven by two heat reservoirs. This model exhibits a spontaneous breaking of symmetry and gives rise to directed transport in the case of a non- vanishing interparticle interaction strength. For strong coupling between the particles we derive an expression for the propagation velocity valid for arbitrary periodic potentials. In the limit of strong coupling the model is equivalent to the B\"uttiker-Landauer model [1-3] for a single particle diffusing in an environment with position dependent temperature. By using numerical calculations of the Fokker-Planck equation and simulations of the Langevin equations we study the model for arbitrary coupling, retrieving many features of the strong coupling limit. In particular, directed transport emerges even for symmetric potentials. For distinct heat reservoirs the heat currents are well-defined quantities allowing a study of the motor efficiency. We show that the optimal working regime occurs for moderate coupling. Finally, we introduce a model with discrete phase space which captures the essential features of the continuous model, can be solved in the limit of weak coupling, and exhibits a larger efficiency than the continuous counterpart.Comment: Revised version. Extended discussion on the discrete model. To appear in EP