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Identification of defective DNA structures is a difficult task, since small differences in base-pair bonding are hidden in the local structural variability of a generally random base-pair sequence. Defects, such as base mismatches, missing bases, crosslinks, and so on, occur in DNA with high frequency and must be efficiently identified and repaired to avoid dire consequences such as genetic mutations. Here, we focus on the detection of base mismatches, which is local deviations from the ideal Watson–Crick pairing rule, which may typically originate from DNA replication process, foreign chemical attack, or ionizing radiation. Experimental detection of a mismatch defect demands the ability to measure slight deviations in the free energy and molecular structure. We introduce different mismatches in short DNA hairpins (10 or 20 base pairs plus a 4-base loop) sandwiched between dsDNA handles to be used in single-molecule force spectroscopy with optical tweezers. We perform both hopping and force-pulling experiments to measure the excess free energies and deduce the characteristic kinetic signatures of the mismatch from the force–distance curves. All-atom molecular dynamics simulations lend support to the detailed interpretation of the experimental data. Such measurements, at the lowest sensitivity limits of this experimental technique, demonstrate the capability of identifying the presence of mismatches in a random complementary dsDNA sequence and provide lower bounds for the ability to distinguish different structural defects. [ABSTRACT FROM AUTHOR]

Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to extract the thermodynamics and kinetics of folding and unfolding reactions. In hopping experiments, a molecule executes transitions between the unfolded and folded states at a preset value of the force [constant force mode (CFM) under force feedback] or trap position [passive mode (PM) without feedback] and the force-dependent kinetic rates extracted from the lifetime of each state (CFM) and the rupture force distributions (PM) using the Bell-Evans model. However, hopping experiments in the CFM are known to overestimate molecular distances and folding free energies for fast transitions compared to the response time of the feedback. In contrast, kinetic rate measurements from pulling experiments have been mostly done in the PM while the CFM is seldom implemented in pulling protocols. Here, we carry out hopping and pulling experiments in a short DNA hairpin in the PM and CFM at three different temperatures (6 °C, 25 °C, and 45 °C) exhibiting largely varying kinetic rates. As expected, we find that equilibrium hopping experiments in the CFM and PM perform well at 6 °C (where kinetics are slow), whereas the CFM overestimates molecular parameters at 45 °C (where kinetics are fast). In contrast, nonequilibrium pulling experiments perform well in both modes at all temperatures. This demonstrates that the same kind of feedback algorithm in the CFM leads to more reliable determination of the folding reaction parameters in irreversible pulling experiments. [ABSTRACT FROM AUTHOR]

Temperature is a well-defined quantity for systems in equilibrium. For glassy systems, it has been extended to the non-equilibrium regime, showing up as an effective quantity in a modified version of the fluctuation-dissipation theorem. However, experimental evidence supporting this definition remains scarce. Here, we present the first direct experimental demonstration of the effective temperature by measuring correlations and responses in single molecules in non-equilibrium steady states generated under external random forces. We combine experiment, analytical theory and simulations for systems with different levels of complexity, ranging from a single bead in an optical trap to two-state and multiple-state DNA hairpins. From these data, we extract a unifying picture for the existence of an effective temperature based on the relative order of various timescales characterizing intrinsic relaxation and external driving. Our study thus introduces driven small systems as a fertile ground to address fundamental concepts in statistical physics, condensed-matter physics and biophysics. [ABSTRACT FROM AUTHOR]

We analyze mean-field models of synchronization of phase oscillators with singular couplings and subject to external random forces. They are related to the Kuramoto–Sakaguchi model. Their probability densities satisfy local partial differential equations similar to the porous medium, Burgers and extended Burgers systems depending on the degree of singularity of the coupling. We show that porous medium oscillators (the most singularly coupled) do not synchronize and that (transient) synchronization is possible only at zero temperature for Burgers oscillators. The extended Burgers oscillators have a nonlocal coupling first introduced by Daido and they may synchronize at any temperature. Exact expressions for their synchronized phases and for Daido's order function are given in terms of elliptic functions. [ABSTRACT FROM AUTHOR]

Atomic force microscopes and optical tweezers are widely used to probe the mechanical properties of individual molecules and molecular interactions, by exerting mechanical forces that induce transitions such as unfolding or dissociation. These transitions often occur under nonequilibrium conditions and are associated with hysteresis effects—features usually taken to preclude the extraction of equilibrium information from the experimental data. But fluctuation theorems allow us to relate the work along nonequilibrium trajectories to thermodynamic free-energy differences. They have been shown to be applicable to single-molecule force measurements and have already provided information on the folding free energy of a RNA hairpin. Here we show that the Crooks fluctuation theorem can be used to determine folding free energies for folding and unfolding processes occurring in weak as well as strong nonequilibrium regimes, thereby providing a test of its validity under such conditions. We use optical tweezers to measure repeatedly the mechanical work associated with the unfolding and refolding of a small RNA hairpin and an RNA three-helix junction. The resultant work distributions are then analysed according to the theorem and allow us to determine the difference in folding free energy between an RNA molecule and a mutant differing only by one base pair, and the thermodynamic stabilizing effect of magnesium ions on the RNA structure. [ABSTRACT FROM AUTHOR]

Most natural processes occur far from equilibrium and cannot be treated within the framework of classical thermodynamics. In 1998, Oono and Paniconi [Oono, Y. & Paniconi,M. (1998) Prog. Theor. Phys. Suppl. 130, 29-44] proposed a general phenomenological framework, steady-state thermodynamics, encompassing non- equilibrium steady states and transitions between such states. In 2001, Hatano and Sasa [Hatano, T. & Sasa, 51(2001) Phys. Rev. Lett. 86, 3463-3466] derived a testable prediction of this theory. Specifically, they were able to show that the exponential average of Y, a quantity similar to a dissipated work, should be equal to zero for arbitrary transitions between nonequilibrium steady states, -ln(e-v) = 0. We have tested this strong prediction by measuring the dissipation and fluctuations of microspheres optically driven through water. We have found that -ln(e-v) 0 for three different nonequilibrium systems, supporting Hatano and Sasa's proposed extension of thermodynamics to arbitrary steady states and irreversible transitions. [ABSTRACT FROM AUTHOR]

We review the use of kinetically constrained models (KCMs) for the study of dynamics in glassy systems. The characteristic feature of KCMs is that they have trivial, often non-interacting, equilibrium behaviour but interesting slow dynamics due to restrictions on the allowed transitions between configurations. The basic question which KCMs ask is therefore how much glassy physics can be understood without an underlying 'equilibrium glass transition'. After a brief review of glassy phenomenology, we describe the main model classes, which include spin-facilitated (Ising) models, constrained lattice gases, models inspired by cellular structures such as soap froths, models obtained via mappings from interacting systems without constraints, and finally related models such as urn, oscillator, tiling and needle models. We then describe the broad range of techniques that have been applied to KCMs, including exact solutions, adiabatic approximations, projection and mode-coupling techniques, diagrammatic approaches and mappings to quantum systems or effective models. Finally, we give a survey of the known results for the dynamics of KCMs both in and out of equilibrium, including topics such as relaxation time divergences and dynamical transitions, nonlinear relaxation, ageing and effective temperatures, cooperativity and dynamical heterogeneities, and finally non-equilibrium stationary states generated by external driving. We conclude with a discussion of open questions and possibilities for future work. [ABSTRACT FROM AUTHOR]

: We propose a new method to compute the configurational entropy of glassy systems as a function of the free energy of valleys at a given temperature, in the framework of the Stillinger and Weber approach. In this method, which we call free-energy inherent structures (FEIS) approach, valleys are represented by inherent structures that are statistically grouped according to their free-energy rather than the energy as is commonly done in the standard procedure. The FEIS method provides a further step toward a description of the relaxational behavior of glassy systems in terms of a free energy measure. It can be used to determine the character of the glass transition as well as the mode coupling and the Kauzmann temperatures. We illustrate the usefulness of the method by applying it to simple models of glasses and spin glasses. [ABSTRACT FROM AUTHOR]

Reports on the use of a two-state kinetic model for investigating the work dissipated during the irreversible unfolding of single molecules by mechanical force. Description of the model; Computation of the probability distribution for the dissipated work; Proportionality of the amount of dissipated work to the rate of application of force and to the relaxation time of the molecule.

We consider a one-dimensional gas of two kinds of particles with different masses interacting through short range interactions. The system exhibits an extreme form of the Soret effect: when the ends of the system are in contact with thermal baths of different temperatures, there is complete separation of the species. We show how this separation can be well described in the Boltzmann approximation and discuss the origin of this odd behavior. [ABSTRACT FROM AUTHOR]

We present a detailed study of the scaling behavior of correlations functions and AC susceptibility relaxations in the aging regime in three-dimensional spin glasses. The agreement between simulations and experiments is excellent confirming the validity of the full aging scenario with weak sub-aging effects. [ABSTRACT FROM AUTHOR]

We study the most suitable procedure to measure the effective temperature in off-equilibrium systems. We analyze the stationary current established between an off-equilibrium system and a thermometer and the necessary conditions for that current to vanish. We find that the thermometer must have a short characteristic time-scale compared to the typical decorrelation time of the glassy system to correctly measure the effective temperature. This general conclusion is confirmed analyzing an ensemble of harmonic oscillators with Monte Carlo dynamics as an illustrative example of a solvable model of a glass. We also find that the current defined allows to extend Fourier's law to the off-equilibrium regime by consistently defining effective transport coefficients. Our results for the oscillator model explain why thermal conductivities between thermalized and frozen degrees of freedom in structural glasses are extremely small. [ABSTRACT FROM AUTHOR]

In order to describe the thermodynamics of the glassy systems it has been recently introduced an extra parameter, the effective temperature which generalizes the fluctuation-dissipation theorem (FDT) to off-equilibrium systems and supposedly describes thermal fluctuations around the aging state. Using this concept we investigate the applicability of a zeroth thermodynamic law for non-equilibrium systems. In particular we study two coupled systems of harmonic oscillators with Monte Carlo dynamics. We analyze in detail two types of dynamics: 1) sequential dynamics where the coupling between the subsystems comes only from the Hamiltonian and 2) parallel dynamics where there is a further coupling between the subsystems arising from the dynamics. We show that the coupling described in the first case is not enough to make asymptotically the effective temperatures of the two interacting subsystems equalize, the reason being the too small thermal conductivity between them in the aging state. This explains why different interacting degrees of freedom in structural glasses may stay at different effective temperatures without never mutually thermalizing. [ABSTRACT FROM AUTHOR]

The use of parameters measuring order-parameter fluctuations (OPF) has been encouraged by the recent results reported in referenece [2,3] which show that two of these parameters, G and Gc, take universal values in the . In this paper we present a detailed study of parameters measuring OPF for two mean-field models with and without time-reversal symmetry which exhibit different patterns of replica symmetry breaking below the transition: the Sherrington-Kirkpatrick model with and without a field and the Ising p-spin glass ( p = 3). We give numerical results and analyze the consequences which replica equivalence imposes on these models in the infinite volume limit. We give evidence for the transition in each system and discuss the character of finite-size effects. Furthermore, a comparative study between this new family of parameters and the usual Binder cumulant analysis shows what kind of new information can be extracted from the finite T behavior of these quantities. The two main outcomes of this work are: 1) Parameters measuring OPF give better estimates than the Binder cumulant for Tc and even for very small systems they give evidence for the transition. 2) For systems with no time-reversal symmetry, parameters defined in terms of connected quantities are the proper ones to look at. [ABSTRACT FROM AUTHOR]

We discuss the relevance of the Stillinger and Weber approach to the glass transition investigating the nonequilibrium behavior of models with nontrivial dynamics, but with simple equilibrium properties. We consider a family of 1D constrained kinetic models, which interpolates between the asymmetric chain introduced by Ja¨ckle and Eisinger [Z. Phys. B 84, 115 (1991)] and the symmetric chain introduced by Fredrickson and Andersen [Phys. Rev. Lett 53, 1244 (1984)], and the 1D version of the Backgammon model [Phys. Rev. Lett. 75, 1190 (1995)]. We show that the configurational entropy obtained from the inherent structures is the same for all models irrespective of their different microscopic dynamics. We present a detailed study of the coarsening behavior of these models, including the relation between fluctuations and response. Our results suggest that any approach to the glass transition inspired by mean-field ideas and resting on the definition of a configurational entropy must rely on the absence of any growing characteristic coarsening pattern. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

While thermal rates of state transitions in classical systems have been studied for almost a century, associated transition-path times have only recently received attention. Uphill and downhill transition paths between states at different free energies should be statistically indistinguishable. Here, we systematically investigate transition-path-time symmetry and report evidence of its breakdown on the molecular- and meso-scale out of equilibrium. In automated Brownian dynamics experiments, we establish first-passage-time symmetries of colloids driven by femtoNewton forces in holographically-created optical landscapes confined within microchannels. Conversely, we show that transitions which couple in a path-dependent manner to fluctuating forces exhibit asymmetry. We reproduce this asymmetry in folding transitions of DNA-hairpins driven out of equilibrium and suggest a topological mechanism of symmetry breakdown. Our results are relevant to measurements that capture a single coordinate in a multidimensional free energy landscape, as encountered in electrophysiology and single-molecule fluorescence experiments. Microscopic transition mechanisms impact many biophysical systems. In this work, the authors explore transition path times between thermodynamic states experimentally, and show symmetry breaking in the transition times under an external force that drives the system out of equilibrium. [ABSTRACT FROM AUTHOR]

We present a dual-trap optical tweezers setup which directly measures forces using linear momentum conservation. The setup uses a counter-propagating geometry, which allows momentum measurement on each beam separately. The experimental advantages of this setup include low drift due to all-optical manipulation, and a robust calibration (independent of the features of the trapped object or buffer medium) due to the force measurement method. Although this design does not attain the high-resolution of some co-propagating setups, we show that it can be used to perform different single molecule measurements: fluctuation-based molecular stiffness characterization at different forces and hopping experiments on molecular hairpins. Remarkably, in our setup it is possible to manipulate very short tethers (such as molecular hairpins with short handles) down to the limit where beads are almost in contact. The setup is used to illustrate a novel method for measuring the stiffness of optical traps and tethers on the basis of equilibrium force fluctuations, i.e., without the need of measuring the force vs molecular extension curve. This method is of general interest for dual trap optical tweezers setups and can be extended to setups which do not directly measure forces. [ABSTRACT FROM AUTHOR]