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

An Ising-Like model for protein mechanical unfolding

The mechanical unfolding of proteins is investigated by extending the Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of freedom, which has proved successful in describing the kinetics of protein folding. Such a model is generalized by including the effect of an external force, and its thermodynamics turns out to be exactly solvable. We consider two molecules, the 27th immunoglobulin domain of titin and protein PIN1. In the case of titin we determine equilibrium force-extension curves and study nonequilibrium phenomena in the frameworks of dynamic loading and force clamp protocols, verifying theoretical laws and finding the position of the kinetic barrier which hinders the unfolding of the molecule. The PIN1 molecule is used to check the possibility of computing the free energy landscape as a function of the molecule length by means of an extended form of the Jarzynski equality.Comment: 4 pages + appendi

Work probability distribution in single molecule experiments

We derive and solve a differential equation satisfied by the probability distribution of the work done on a single biomolecule in a mechanical unzipping experiment. The unzipping is described as a thermally activated escape process in an energy landscape. The Jarzynski equality is recovered as an identity, independent of the pulling protocol. This approach allows one to evaluate easily, by numerical integration, the work distribution, once a few parameters of the energy landscape are known.Comment: To appear on EP

Energetics and performance of a microscopic heat engine based on exact calculations of work and heat distributions

We investigate a microscopic motor based on an externally controlled two-level system. One cycle of the motor operation consists of two strokes. Within each stroke, the two-level system is in contact with a given thermal bath and its energy levels are driven with a constant rate. The time evolution of the occupation probabilities of the two states are controlled by one rate equation and represent the system's response with respect to the external driving. We give the exact solution of the rate equation for the limit cycle and discuss the emerging thermodynamics: the work done on the environment, the heat exchanged with the baths, the entropy production, the motor's efficiency, and the power output. Furthermore we introduce an augmented stochastic process which reflects, at a given time, both the occupation probabilities for the two states and the time spent in the individual states during the previous evolution. The exact calculation of the evolution operator for the augmented process allows us to discuss in detail the probability density for the performed work during the limit cycle. In the strongly irreversible regime, the density exhibits important qualitative differences with respect to the more common Gaussian shape in the regime of weak irreversibility.Comment: 21 pages, 7 figure

Discrete Breathers in a Realistic Coarse-Grained Model of Proteins

We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. In the case of the small $\beta$-barrel structure that we consider, localization occurs on the turns connecting the strands. At high energies, discrete breathers stabilize the structure by concentrating energy on few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of this two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.Comment: Submitted to Physical Biolog

Aging in lattice-gas models with constrained dynamics

We investigate the aging behavior of lattice-gas models with constrained dynamics in which particle exchange with a reservoir is allowed. Such models provide a particularly simple interpretation of aging phenomena as a slow approach to criticality. They appear as the simplest three dimensional models exhibiting a glassy behavior similar to that of mean field (low temperature mode-coupling) models.Comment: 5 pages and 3 figures, REVTeX. Submitted to Europhysics Letter

A volume inequality for quantum Fisher information and the uncertainty principle

Let $A_1,...,A_N$ be complex self-adjoint matrices and let $\rho$ be a density matrix. The Robertson uncertainty principle $$det(Cov_\rho(A_h,A_j)) \geq det(- \frac{i}{2} Tr(\rho [A_h,A_j]))$$ gives a bound for the quantum generalized covariance in terms of the commutators $[A_h,A_j]$. The right side matrix is antisymmetric and therefore the bound is trivial (equal to zero) in the odd case $N=2m+1$. Let $f$ be an arbitrary normalized symmetric operator monotone function and let $_{\rho,f}$ be the associated quantum Fisher information. In this paper we conjecture the inequality $$det (Cov_\rho(A_h,A_j)) \geq det (\frac{f(0)}{2} _{\rho,f})$$ that gives a non-trivial bound for any natural number $N$ using the commutators $i[\rho, A_h]$. The inequality has been proved in the cases $N=1,2$ by the joint efforts of many authors. In this paper we prove the case N=3 for real matrices

Entropy production for mechanically or chemically driven biomolecules

Entropy production along a single stochastic trajectory of a biomolecule is discussed for two different sources of non-equilibrium. For a molecule manipulated mechanically by an AFM or an optical tweezer, entropy production (or annihilation) occurs in the molecular conformation proper or in the surrounding medium. Within a Langevin dynamics, a unique identification of these two contributions is possible. The total entropy change obeys an integral fluctuation theorem and a class of further exact relations, which we prove for arbitrarily coupled slow degrees of freedom including hydrodynamic interactions. These theoretical results can therefore also be applied to driven colloidal systems. For transitions between different internal conformations of a biomolecule involving unbalanced chemical reactions, we provide a thermodynamically consistent formulation and identify again the two sources of entropy production, which obey similar exact relations. We clarify the particular role degenerate states have in such a description

Nonparametric Information Geometry

The differential-geometric structure of the set of positive densities on a given measure space has raised the interest of many mathematicians after the discovery by C.R. Rao of the geometric meaning of the Fisher information. Most of the research is focused on parametric statistical models. In series of papers by author and coworkers a particular version of the nonparametric case has been discussed. It consists of a minimalistic structure modeled according the theory of exponential families: given a reference density other densities are represented by the centered log likelihood which is an element of an Orlicz space. This mappings give a system of charts of a Banach manifold. It has been observed that, while the construction is natural, the practical applicability is limited by the technical difficulty to deal with such a class of Banach spaces. It has been suggested recently to replace the exponential function with other functions with similar behavior but polynomial growth at infinity in order to obtain more tractable Banach spaces, e.g. Hilbert spaces. We give first a review of our theory with special emphasis on the specific issues of the infinite dimensional setting. In a second part we discuss two specific topics, differential equations and the metric connection. The position of this line of research with respect to other approaches is briefly discussed.Comment: Submitted for publication in the Proceedings od GSI2013 Aug 28-30 2013 Pari

Onsager-Machlup theory for nonequilibrium steady states and fluctuation theorems

A generalization of the Onsager-Machlup theory from equilibrium to nonequilibrium steady states and its connection with recent fluctuation theorems are discussed for a dragged particle restricted by a harmonic potential in a heat reservoir. Using a functional integral approach, the probability functional for a path is expressed in terms of a Lagrangian function from which an entropy production rate and dissipation functions are introduced, and nonequilibrium thermodynamic relations like the energy conservation law and the second law of thermodynamics are derived. Using this Lagrangian function we establish two nonequilibrium detailed balance relations, which not only lead to a fluctuation theorem for work but also to one related to energy loss by friction. In addition, we carried out the functional integrals for heat explicitly, leading to the extended fluctuation theorem for heat. We also present a simple argument for this extended fluctuation theorem in the long time limit.Comment: 20 pages, 2 figure