arXiv subjects

F. Ritort

Publications and source records attributed to F. Ritort.

At least 37 records · Page 2Linked to original sources

arXiv2007

Nonequilibrium fluctuations in small systems: From physics to biology

In this paper I am presenting an overview on several topics related to nonequilibrium fluctuations in small systems. I start with a general discussion about fluctuation theorems and applications to physical examples extracted from physics and biology: a bead in an optical trap and single molecule force experiments. Next I present a general discussion on path thermodynamics and consider distributions of work/heat fluctuations as large deviation functions. Then I address the topic of glassy dynamics from the perspective of nonequilibrium fluctuations due to small cooperatively rearranging regions. Finally, I conclude with a brief digression on future perspectives.

cond-mat.stat-mech↗

arXiv2006

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.

cond-mat.soft↗

arXiv2006

Force dependent fragility in RNA hairpins

We apply Kramers theory to investigate the dissociation of multiple bonds under mechanical force and interpret experimental results for the unfolding/refolding force distributions of an RNA hairpin pulled at different loading rates using laser tweezers. We identify two different kinetic regimes depending on the range of forces explored during the unfolding and refolding process. The present approach extends the range of validity of the two-states approximation by providing a theoretical framework to reconstruct free-energy landscapes and identify force-induced structural changes in molecular transition states using single molecule pulling experiments. The method should be applicable to RNA hairpins with multiple kinetic barriers.

cond-mat.soft↗

arXiv2006

Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers

When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension curves (FECs). A characteristic plateau force (around 10 pN) and hysteresis between the pulling and relaxation cycles are observed for different dendrimer sizes, indicating the existence of a first-order transition between two phases (condensed and extended) of the fiber. The fact that we can reproduce the same FECs in the absence of additional dendrimers in the buffer medium indicates that dendrimers remain irreversibly bound to the DNA backbone. Upon salt variation FECs change noticeably confirming that electrostatic forces drive the condensation transition. Finally, we propose a simple model for the decondensing transition that qualitatively reproduces the FECs and which is confirmed by AFM images.

cond-mat.soft↗

arXiv2005

Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies

The description of nonequilibrium processes in nano-sized objects, where the typical energies involved are a few times, is increasingly becoming central to disciplines as diverse as condensed-matter physics, materials science, and biophysics. Major recent developments towards a unified treatment of arbitrarily large fluctuations in small systems are described by fluctuation theorems that relate the probabilities of a system absorbing from or releasing to the bath a given amount of energy in a nonequilibrium process. Here we experimentally verify the Crooks Fluctuation Theorem (CFT) under weak and strong nonequilibrium conditions by using optical tweezers to measure the irreversible mechanical work during the unfolding and refolding of a small RNA hairpin and an RNA three-helix junction. We also show that the CFT provides a powerful way to obtain folding free energies in biomolecules by determining the crossing between the unfolding and refolding irreversible work distributions. The method makes it possible to obtain folding free energies in nonequilibrium processes that dissipate up to of the average total work exerted, thereby paving the way for reconstructing free energy landscapes along reaction coordinates in nonequilibrium single-molecule experiments.

cond-mat.stat-mech↗

arXiv2005

The Nonequilibrium Thermodynamics of Small Systems

The interactions of tiny objects with their environment are dominated by thermal fluctuations. Guided by theory and assisted by micromanipulation tools, scientists have begun to study such interactions in detail.

cond-mat.stat-mech↗

arXiv2005

Universality of Fluctuation-Dissipation Ratios: The Ferromagnetic Model

We calculate analytically the fluctuation-dissipation ratio (FDR) for Ising ferromagnets quenched to criticality, both for the long-range model and its short-range analogue in the limit of large dimension. Our exact solution shows that, for both models, $X^\infty=1/2$ if the system is unmagnetized while $X^\infty=4/5$ if the initial magnetization is non-zero. This indicates that two different classes of critical coarsening dynamics need to be distinguished depending on the initial conditions, each with its own nontrivial FDR. We also analyze the dependence of the FDR on whether local and global observables are used. These results clarify how a proper local FDR (and the corresponding effective temperature) should be defined in long-range models in order to avoid spurious inconsistencies and maintain the expected correspondence between local and global results; global observables turn out to be far more robust tools for detecting non-equilibrium FDRs.

cond-mat.stat-mech↗

arXiv2005

Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems

Biomolecules carry out very specialized tasks inside the cell where energies involved are few tens of k_BT, small enough for thermal fluctuations to be relevant in many biomolecular processes. In this paper I discuss a few concepts and present some experimental results that show how the study of fluctuation theorems applied to biomolecules contributes to our understanding of the nonequilibrium thermal behavior of small systems.

cond-mat.stat-mech↗

arXiv2005

Mode-Dependent nonequilibrium temperature in aging systems

We introduce an exactly solvable model for glassy dynamics with many relaxational modes, each one characterized by a different relaxational time-scale. Analytical solution of the aging dynamics at low temperatures shows that a nonequilibrium or effective temperature can be associated to each time-scale or mode. The spectrum of effective temperatures shows two regions that are separated by an age dependent boundary threshold. Region I is characterized by partially equilibrated modes that relax faster than the modes at the threshold boundary. Thermal fluctuations and time-correlations for modes in region I show that those modes are in mutual thermal equilibrium at a unique age-dependent effective temperature $Θ(s)$. In contrast, modes with relaxational timescales longer than that of modes at the threshold (region II) show diffusive properties and do not share the common temperature $Θ(s)$. The shift of the threshold toward lower energy modes as the system ages, and the progressive shrinking of region II, determines how the full spectrum of modes equilibrates. As is usually done in experiments, we have defined a frequency-dependent effective temperature and we have found that all modes in region I are mutually equilibrated at the temperature $Θ(s)$ independently of the probing frequency. The present model aims to explain transport anomalies observed in supercooled liquids in terms of a collection of structurally disordered and cooperative rearranging mesoscopic regions.

cond-mat.stat-mech↗

arXiv2005

Resonant nonequilibrium temperatures

We investigate nonequilibrium temperatures in a two-state system driven to a nonequilibrium steady state by the action of an oscillatory field. The nonequilibrium temperature is determined by coupling a small cavity or probe to the nonequilibrium system and studying the fluctuating noise in the cavity, as has been proposed in the context of glassy systems. We show the presence of resonant effects in the nonequilibrium temperature and discuss the existence of a constitutive steady-state equation in such nonequilibrium conditions. We propose this simple model as an excellent system to carry out experimental measurements of nonequilibrium temperatures. This may help to better understand the physical meaning of this elusive concept.

cond-mat.stat-mech↗

arXiv2004

Spontaneous relaxation in generalized oscillator models with glassy dynamics

In this paper we introduce the generalized oscillator model (GOM) as a family of exactly solvable models useful to investigate theoretical aspects related to the statistical description of the aging state. GOMs are defined by a potential function V(x) and characterized by a zero-temperature relaxation determined by entropy barriers and partial equilibration. Analytic expressions for the effective temperature can be derived using a fluctuation theorem valid in the aging regime without the need to solve the dynamical equations for correlations and responses. Two classes of models are investigated in detail: the homogeneous potential model with V(x)=(k/2p)x^{2p} (p being a positive integer) and the wedge potential model (V(x)=k|x|) where V(x) has a singularity at the ground state coordinate x=0. For the latter, we present some numerical simulations that reinforce the validity of the main analytical results. GOMs offer a conceptual framework to develop a statistical description of the spontaneous relaxation process that has been recently proposed to be at the root of the intermittency phenomenon observed in glasses and colloids.

cond-mat.stat-mech↗

arXiv2004

Work and heat fluctuations in two-state systems: a trajectory thermodynamics formalism

Two-state models provide phenomenological descriptions of many different systems, ranging from physics to chemistry and biology. We investigate work fluctuations in an ensemble of two-state systems driven out of equilibrium under the action of an external perturbation. We calculate the probability density P(W) that a work equal to W is exerted upon the system along a given non-equilibrium trajectory and introduce a trajectory thermodynamics formalism to quantify work fluctuations in the large-size limit. We then define a trajectory entropy S(W) that counts the number of non-equilibrium trajectories P(W)=exp(S(W)/kT) with work equal to W. A trajectory free-energy F(W) can also be defined, which has a minimum at a value of the work that has to be efficiently sampled to quantitatively test the Jarzynski equality. Within this formalism a Lagrange multiplier is also introduced, the inverse of which plays the role of a trajectory temperature. Our solution for P(W) exactly satisfies the fluctuation theorem by Crooks and allows us to investigate heat-fluctuations for a protocol that is invariant under time reversal. The heat distribution is then characterized by a Gaussian component (describing small and frequent heat exchange events) and exponential tails (describing the statistics of large deviations and rare events). For the latter, the width of the exponential tails is related to the aforementioned trajectory temperature. Finite-size effects to the large-N theory and the recovery of work distributions for finite N are also discussed. Finally, we pay particular attention to the case of magnetic nanoparticle systems under the action of a magnetic field H where work and heat fluctuations are predicted to be observable in ramping experiments in micro-SQUIDs.

cond-mat.stat-mech↗

arXiv2004

Work fluctuations, transient violations of the second law and free-energy recovery methods: Perspectives in Theory and Experiments

In this report I discuss fluctuation theorems and transient violations of the second law of thermodynamics in small systems. Special emphasis is placed on free-energy recovery methods in the framework of non-equilibrium single-molecule pulling experiments. The treatment is done from a unified theoretical-experimental perspective and emphasizes how these experiments contribute to our understanding of the thermodynamic behavior of small systems

cond-mat.stat-mech↗

arXiv2003

Stimulated and spontaneous relaxation in glassy systems

Recent numerical simulations of a disordered system (Preprint arXiv:condmat/0307554) have shown the existence of two different relaxational processes (called stimulated and spontaneous) characterizing the relaxation observed in structural glasses. The existence of these two processes has been claimed to be at the roots of the intermittency phenomenon observed in recent experiments. Here we consider a generic system put in contact with a bath at temperature T and characterized by an adiabatic slow relaxation (i.e. by a negligible net heat flow from the system to the bath) in the aging state. We focus on a simplified scenario (termed as partial equilibration) characterized by the fact that $=0 (where only the spontaneous process is observable) and whose microscopic stochastic dynamics is ergodic when constrained to the constant energy surface. Three different effective temperatures can be defined: a) from the fluctuation-dissipation theorem (FDT), b) from a fluctuation theorem describing the statistical distribution of heat exchange events between system and bath and c) from a set of observable-dependent microcanonical relations in the aging state. In a partial equilibration scenario we show how all three temperatures coincide reinforcing the idea that a statistical (rather than thermometric) definition of a non-equilibrium temperature is physically meaningful in aging systems. These results are explicitly checked in a simple model system

cond-mat.dis-nn↗

arXiv2003

Frequency-domain study of relaxation in a spin glass model for the structural glass transition

We have computed the time-dependent susceptibility for the finite-size mean-field Random Orthogonal model (ROM). We find that for temperatures above the mode-coupling temperature the imaginary part of the susceptibility $χ''(ν)$ obeys the scaling forms proposed for glass-forming liquids. Furthermore, as the temperature is lowered the peak frequency of $χ''$ decreases following a Vogel-Fulcher law with a critical temperature remarkably close to the known critical temperature $T_c$ where the configurational entropy vanishes.

cond-mat.stat-mech↗

arXiv2003

Universal dependence of the fluctuation-dissipation ratio on the transition rates in trap models

We investigate violations of the fluctuation-dissipation theorem in two classes of trap models by studying the influence of the perturbing field on the transition rates. We show that for perturbed rates depending upon the value of the observable at the arrival trap, a limiting value of the fluctuation-dissipation ratio does exist. However, the mechanism behind the emergence of this value is different in both classes of models. In particular, for an entropically governed dynamics (where the perturbing field shifts the relative population of traps according to the value of the observable) perturbed rates are argued to take a form that guarantees the existence of a limiting value for the effective temperature, utterly related to the exponential character of the distribution of trap energies. Fluctuation-dissipation (FD) plots reproduce some of the patterns found in a broad class of glassy systems, reinforcing the idea that structural glasses self-generate a dynamical measure that is captured by phenomenological trap models.

cond-mat.dis-nn↗

arXiv2003

Violation of the fluctuation-dissipation theorem in glassy systems: basic notions and the numerical evidence

This review reports on the research done during the 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 currently 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.

cond-mat.dis-nn↗

arXiv2003

A New Method to Compute the Configurational Entropy in Spin Glasses

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.

cond-mat.dis-nn↗