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The same system can exhibit a completely different dynamical behavior when it evolves in equilibrium conditions or when it is driven out-of-equilibrium by, e.g., connecting some of its components to heat baths kept at different temperatures. Here we concentrate on an analytically solvable and experimentally-relevant model of such a system -- the so-called Brownian gyrator -- a two-dimensional nanomachine that performs a systematic, on average, rotation around the origin under non-equilibrium conditions, while no net rotation takes place in equilibrium. On this example, we discuss a question whether it is possible to distinguish between two types of a behavior judging not upon the statistical properties of the trajectories of components, but rather upon their respective spectral densities. The latter are widely used to characterize diverse dynamical systems and are routinely calculated from the data using standard built-in packages. From such a perspective, we inquire whether the power spectral densities possess some "fingerprint" properties specific to the behavior in non-equilibrium. We show that indeed one can conclusively distinguish between equilibrium and non-equilibrium dynamics by analyzing the cross-correlations between the spectral densities of both components in the short frequency limit, or from the spectral densities of both components evaluated at zero frequency. Our analytical predictions, corroborated by experimental and numerical results, open a new direction for the analysis of a non-equilibrium dynamics., Comment: 23 pages, 6 figures

In this chapter, we illustrate recently obtained thermodynamic bounds for a number of enzymatic networks by focusing on simple examples of unicyclic or multi-cyclic networks. We also derive complementary relations which constrain the fluctuations of first-passage times to reach a threshold current.

We consider a molecular machine described as a Brownian particle diffusing in a tilted periodic potential. We evaluate the absorbed and released power of the machine as a function of the applied molecular and chemical forces, by using the fact that the times for completing a cycle in the forward and the backward direction have the same distribution, and that the ratio of the corresponding splitting probabilities can be simply expressed as a function of the applied force. We explicitly evaluate the efficiency at maximum power for a simple sawtooth potential. We also obtain the efficiency at maximum power for a broad class of 2-D models of a Brownian machine and find that loosely coupled machines operate with a smaller efficiency at maximum power than their strongly coupled counterparts., Comment: To appear in EPL

We consider the relation between the microscopic and effective descriptions of the unfolding experiment on a model polypeptide. We evaluate the probability distribution function of the performed work by Monte Carlo simulations and compare it with that obtained by evaluating the work distribution generating function on an effective Brownian motion model tailored to reproduce exactly the equilibrium properties. The agreement is satisfactory for fast protocols, but deteriorates for slower ones, hinting at the existence of processes on several time scales even in such a simple system., Comment: To appear in Physical Biology, Special issue: Polymer physics of the cell

We review and discuss the equations governing the distribution of work done on a system which is driven out of equilibrium by external manipulation, as well as those governing the entropy flow to a reservoir in a nonequilibrium system. We take advantage of these equations to investigate the path phase transition in a manipulated mean-field Ising model and the large-deviation function for the heat flow in the asymmetric exclusion process with periodically varying transition probabilities., Comment: Contribution to Proceedings of "Work, Dissipation, and Fluctuations in Nonequilibrium Physics", Brussels, 2006

We analyze the equations governing the evolution of distributions of the work and the heat exchanged with the environment by a manipulated stochastic system, by means of a compact and general derivation. We obtain explicit solutions for these equations for the case of a dragged Brownian particle in a harmonic potential. We successfully compare the resulting predictions with the outcomes of experiments, consisting in dragging a micron-sized colloidal particle through water with a laser trap.

We argue that the apparent failure of the work-Hamiltonian connection for free energy calculations reported by Vilar and Rubi' (cond-mat arXiv:0704.0761v2) stems from their incorrect expression for the work.

We obtain a simple direct derivation of the differential equation governing the entropy flow probability distribution function of a stochastic system first obtained by Lebowitz and Spohn. Its solution agrees well with the experimental results of Tietz et al [2006 {\it Phys. Rev. Lett.} {\bf 97} 050602]. A trajectory-sampling algorithm allowing to evaluate the entropy flow distribution function is introduced and discussed. This algorithm turns out to be effective at finite times and in the case of time-dependent transition rates, and is successfully applied to an asymmetric simple exclusion process.

A refinement of an argument due to Maxwell for the equipartition of kinetic energy in a mixture of ideal gases with different masses is proposed. The argument is elementary, yet it may work as an illustration of the role of symmetry and independence postulates in kinetic theory.

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.

A fluctuation relation, which is an extended form of the Jarzynski equality, is introduced and discussed. We show how to apply this relation in order to evaluate the free energy landscape of simple systems. These systems are manipulated by varying the external field coupled with a systems' internal characteristic variable. Two different manipulation protocols are here considered: in the first case the external field is a linear function of time, in the second case it is a periodic function of time. While for simple mean field systems both the linear protocol and the oscillatory protocol provide a reliable estimate of the free energy landscape, for a simple model ofhomopolymer the oscillatory protocol turns out to be not reliable for this purpose. We then discuss the possibility of application of the method here presented to evaluate the free energy landscape of real systems, and the practical limitations that one can face in the realization of an experimental set-up.

We derive the differential equation describing the time evolution of the work probability distribution function of a stochastic system which is driven out of equilibrium by the manipulation of a parameter. We consider both systems described by their microscopic state or by a collective variable which identifies a quasiequilibrium state. We show that the work probability distribution can be represented by a path integral, which is dominated by ``classical'' paths in the large system size limit. We compare these results with simulated manipulation of mean-field systems. We discuss the range of applicability of the Jarzynski equality for evaluating the system free energy using these out-of-equilibrium manipulations. Large fluctuations in the work and the shape of the work distribution tails are also discussed.

We generalize Galam's model of opinion spreading by introducing three competing choices. At each update, the population is randomly divided in groups of three agents, whose members adopt the opinion of the local majority. In the case of a tie, the local group adopts opinion A, B or C with probabilities alpha, beta and (1-alpha-beta) respectively. We derive the associated phase diagrams and dynamics by both analytical means and simulations. Polarization is always reached within very short time scales. We point out situations in which an initially very small minority opinion can invade the whole system., Comment: To appear in European Physical Journal B. A few errors corrected, some figures redrawn from the first version

We consider a mean-field system described by a general collective variable $M$, driven out of equilibrium by the manipulation of a parameter $\mu$. Given a general dynamics compatible with its equilibrium distribution, we derive the evolution equation for the joint probability distribution function of $M$ and the work $W$ done on the system. We solve this equation by path integrals. We show how the Jarzynski equality holds identically at the path integral level and for the classical paths which dominate the expression in the thermodynamic limit. We discuss some implications of our results., Comment: 4 pages, 2 figures; accepted for publication in Europhys. Lett

It is shown that the various claims made in the comment by M. Ya. Azbel (physics/0403106) on the two publications Phys. Rev. Lett. 91, 055502 (2003) and Phys. Rev. Lett. 85, 4988 (2000) are invalid. They are a result of a misinterpretation of the main points of both papers.

It is shown that the scaling analysis presented in Phys. Rev. Lett. 85, 4988 (2000) is valid for finite chains of lengths relevant to experiments, in contrast to a recent claim made by A. Hanke and R. Metzler in cond-mat/0110164.

We discuss a population of sequences subject to mutations and frequency-dependent selection, where the fitness of a sequence depends on the composition of the entire population. This type of dynamics is crucial to understand the evolution of genomic regulation. Mathematically, it takes the form of a reaction-diffusion problem that is nonlinear in the population state. In our model system, the fitness is determined by a simple mathematical game, the hawk-dove game. The stationary population distribution is found to be a quasispecies with properties different from those which hold in fixed fitness landscapes., Comment: 7 pages, 2 figures. Typos corrected, references updated. An exact solution for the hawks-dove game is provided

It is shown that the scaling analysis presented in Phys. Rev. Lett. 85, 4988 (2000) (cond-mat/0007141) is valid for finite chains of lengths relevant to experiments, in contrast to a recent claim made by A. Hanke and R. Metzler in cond-mat/0108323.

We introduce a general framework to study the processivity of molecular motors moving along a polar filament and discuss the average time spent attached to the filament as a function of a tangentially applied load. Our study of specific models suggests that the attachment time of a motor decreases with increasing ATP concentration and that double-headed motors such as kinesins lose their processivity under forcing conditions while processive single-headed motors are less sensitive to tangential forcing., Comment: 7 pages, 5 figures. To be published on Europhysics Letters

Experimental studies of the thermal denaturation of DNA yield a strong indication that the transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic configurations of a DNA molecule are given by an alternating sequence of non-interacting bound segments and denaturated loops. Studies of these models neglect the repulsive, self-avoiding, interaction between different loops and segments and have invariably yielded continuous denaturation transitions. In this study we exploit recent results on scaling properties of polymer networks of arbitrary topology in order to take into account the excluded-volume interaction between denaturated loops and the rest of the chain. We thus obtain a first-order phase transition in d=2 dimensions and above, in agreement with experiments. We also consider within our approach the unzipping transition, which takes place when the two DNA strands are pulled apart by an external force acting on one end. We find that the unzipping transition is also first order. Although the denaturation and unzipping transitions are thermodynamically first order, they do exhibit critical fluctuations in some of their properties. For instance, the loop size distribution decays algebraically at the transition and the length of the denaturated end segment diverges as the transition is approached. We evaluate these critical properties within our approach., Comment: 12pages,8 figures, REVTEX4

We evaluate the effective Hamiltonian governing, at the optically resolved scale, the elastic properties of micro-manipulated membranes. We identify floppy, entropic-tense and stretched-tense regimes, representing different behaviors of the effective area-elasticity of the membrane. The corresponding effective tension depends on the microscopic parameters (total area, bending rigidity) and on the optically visible area, which is controlled by the imposed external constraints. We successfully compare our predictions with recent data on micropipette experiments., Comment: To be published in Phys. Rev. Lett

We discuss the response of aging systems with short-range interactions to a class of random perturbations. Although these systems are out of equilibrium, the limit value of the free energy at long times is equal to the equilibrium free energy. By exploiting this fact, we define a new order parameter function, and we relate it to the ratio between response and fluctuation, which is in principle measurable in an aging experiment. For a class of systems possessing stochastic stability, we show that this new order parameter function is intimately related to the static order parameter function, describing the distribution of overlaps between clustering states. The same method is applied to investigate the geometrical organization of pure states. We show that the ultrametric organization in the dynamics implies static ultrametricity, and we relate these properties to static separability, i.e., the property that the measure of the overlap between pure states is essentially unique. Our results, especially relevant for spin glasses, pave the way to an experimental determination of the order parameter function., Comment: 17 pages

We consider the effects of the coupling between the orientational order of the two monolayers in flat nematic bilayers. We show that the presence of a topological defect on one bilayer generates a nontrivial orientational texture on both monolayers. Therefore, one cannot consider isolated defects on one monolayer, but rather associated pairs of defects on either monolayer, which we call bi-defects. Bi-defects generally produce walls, such that the textures of the two monolayers are identical outside the walls, and different in their interior. We suggest some experimental conditions in which these structures could be observed., Comment: RevTeX, 4 pages, 3 figures

Altruistic behaviour is disadvantageous for the individual while is advantageous for its group. If the target of the selection is the individual, one would expect the selection process to lead to populations formed by wholly homogeneous groups, made up of either altruistic or egoistic individuals, where the winning choice depends on the balance beetwen group advantage and individual disadvantage. We show in a simple model that populations formed by inhomogeneous groups can be stabilized in some circumstances. We argue that this condition is realized when there is a relative advantage conferred by the presence of a few altruists to all the members of the group., Comment: 11 pages, 5figs, LaTeX, REVTeX

We consider the Derrida-Higgs (DH) statistical model of species formation in the case where the population is geographically distributed in discrete locations, and mating only takes place within one location. Keeping the rate of migration between neighbouring locations at a fixed value, we change the mutation rate, changing therefore the average overlap between genotypes. When the overlap between individuals living in different locations falls below a fecundity threshold, speciation occurs. When more species coexist, the genetic structure of the population (as described by the overlap distribution $P(q)$) fluctuates. However, the average overlap, both within one location and among neighbouring locations, appears to vary according to the same laws as in the absence of speciation. The model provides a reasonable estimate of the parameter values necessary to observe geographic speciation, which is found to be much more likely than the sympatric speciation of the original DH model. Applications to the case of circular invasion, where the concept of biological species appears to run into difficulties, are sketched., Comment: 11, IOPTeX