Aging in a simple model of a structural glass

We consider a simple model of a structural glass, represented by a lattice gas with kinetic constraints in contact with a particle reservoir. Quench below the glass transition is represented by the jump of the chemical potential above a threshold. After a quench, the density approaches the critical density-where the diffusion coefficient of the particles vanishes-following a power law in time. In this regime, the two-time self-correlation functions exhibit aging. The behavior of the model can be understood in terms of simple mean-field arguments.Comment: LaTeX, 8 pages, 4 figures. Contribution to the Conference "Disorder and Chaos", Rome, September 1997. A few misprints corrected, and references update

The distribution function of entropy flow in stochastic systems

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

Evaluation of free energy landscapes from manipulation experiments

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

Thermodynamics of accuracy in kinetic proofreading: Dissipation and efficiency trade-offs

The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide a consistent thermodynamic description of enzyme-assisted assembly processes involving competing substrates, in a Master Equation framework. We introduce and evaluate a measure of the efficiency based on rigorous non-equilibrium inequalities. The performance of several proofreading models are thus analyzed and the related time, dissipation and efficiency vs. error trade-offs exhibited for different discrimination regimes. We finally introduce and analyze in the same framework a simple model which takes into account correlations between consecutive enzyme-assisted assembly steps. This work highlights the relevance of the distinction between energetic and kinetic discrimination regimes in enzyme-substrate interactions.Comment: IOP Class, 20 pages, 9 figure