1,721,021 research outputs found
Violation of the fluctuation-dissipation theorem in glassy systems: basic notions and the numerical evidence
No full textThis review reports on the research done during past years on violations of the fluctuation–dissipation theorem (FDT) in glassy systems. It is focused on the existence of a quasi-fluctuation–dissipation theorem (QFDT) in glassy systems and the current supporting knowledge gained from numerical simulation studies. It covers a broad range of non-stationary aging and stationary driven systems such as structural glasses, spin glasses, coarsening systems, ferromagnetic models at criticality, trap models, models with entropy barriers, kinetically constrained models, sheared systems and granular media. The review is divided into four main parts: (1) an introductory section explaining basic notions related to the existence of the FDT in equilibrium and its possible extension to the glassy regime (QFDT), (2) a description of the basic analytical tools and results derived in the framework of some exactly solvable models, (3) a detailed report of the current evidence in favour of the QFDT and (4) a brief digression on the experimental evidence in its favour. This review is intended for inexpert readers who want to learn about the basic notions and concepts related to the existence of the QFDT as well as for the more expert readers who may be interested in more specific results
Variance sum rule: proofs and solvable models
Full text linkWe derive, in more general conditions, a recently introduced variance sum rule (VSR) (Di Terlizzi et al 2024 Science 383 971) involving variances of displacement and force impulse for overdamped Langevin systems in a nonequilibrium steady state (NESS). This formula allows visualising the effect of nonequilibrium as a deviation of the sum of variances from normal diffusion 2Dt, with D the diffusion constant and t the time. From the VSR, we also derive formulas for the entropy production rate sigma that, differently from previous results, involve second-order time derivatives of position correlation functions. This novel feature gives a criterion for discriminating strong nonequilibrium regimes without measuring forces. We then apply and discuss our results to three analytically solved models: a stochastic switching trap, a Brownian vortex, and a Brownian gyrator. Finally, we compare the advantages and limitations of known and novel formulas for sigma in an overdamped NESS
Sugar-pucker force-induced transition in single-stranded DNA
Full text linkThe accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples range from DNA hybridization, DNA ligand binding, DNA unwinding by helicases, etc. To date, ssDNA elasticity has been studied with different methods in molecules of varying sequence and contour length. A dispersion of results has been reported and the value of the persistence length has been found to be larger for shorter ssDNA molecules. We carried out pulling experiments with optical tweezers to characterize the elastic response of ssDNA over three orders of magnitude in length (60–14 k bases). By fitting the force-extension curves (FECs) to the Worm-Like Chain model we confirmed the above trend:the persistence length nearly doubles for the shortest molecule (60 b) with respect to the longest one (14 kb). We demonstrate that the observed trend is due to the different force regimes fitted for long and short molecules, which translates into two distinct elastic regimes at low and high forces. We interpret this behavior in terms of a force-induced sugar pucker conformational transition (C3′-endo to C2′-endo) upon pulling ssDNA
Force dependence of proteins’ transition state position and the bell–evans model
Full text linkSingle-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and measure their free energy landscape. The force–extension curves of single proteins often present large hysteresis, with unfolding forces that are higher than refolding ones. Therefore, the high energy of the transition state (TS) in these molecules precludes kinetic rates measurements in equilibrium hopping experiments. In irreversible pulling experiments, force-dependent kinetic rates measurements show a systematic discrepancy between the sum of the folding and unfolding TS distances derived by the kinetic Bell–Evans model and the full molecular extension predicted by elastic models. Here, we show that this discrepancy originates from the force-induced movement of TS. Specifically, we investigate the highly kinetically stable protein barnase, using pulling experiments and the Bell–Evans model to characterize the position of its kinetic barrier. Experimental results show that while the TS stays at a roughly constant distance relative to the native state, it shifts with force relative to the unfolded state. Interestingly, a conversion of the protein extension into amino acid units shows that the TS position follows the Leffler–Hammond postulate: the higher the force, the lower the number of unzipped amino acids relative to the native state. The results are compared with the quasi-reversible unfolding–folding of a short DNA hairpin
Aging effects and dynamic scaling in the 3D Edwards-Anderson spin glasses: a comparison with experiments
No full textDerivation of the spin-glass order parameter from stochastic thermodynamics
No full textA fluctuation relation is derived to extract the order parameter function q(x) in weakly ergodic systems. The relation is based on measuring and classifying entropy production fluctuations according to the value of the overlap q between configurations. For a fixed value of q, entropy production fluctuations are Gaussian distributed allowing us to derive the quasi-FDT so characteristic of aging systems. The theory is validated by extracting the q(x) in various types of glassy models. It might be generally applicable to other nonequilibrium systems and experimental small systems
Glassy Mean-Field Dynamics of the Backgammon model
No full textIn this paper we present an exact study of the relaxation dynamics of the backgammon model. This is a model of a gas of particles in a discrete space which presents glassy phenomena as a result of entropy barriers in configuration space. The model is simple enough to allow for a complete analytical treatment of the dynamics in infinite dimensions. We first derive a closed equation describing the evolution of the occupation number probabilities, then we generalize the analysis to the study the autocorrelation function. We also consider possible variants of the model which allow to study the effect of energy barriers. Typeset using REVT E X I. INTRODUCTION The nature of the glass transition is still poorly understood [1,2]. Under slow cooling real glasses reach a metastable phase of free energy larger than that of the crystal phase. Glasses show a strong slowing down of the dynamics when the temperature is lowered and the transport coefficients increase by several orders of magnitude i..
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