arXiv subjects

Felix Ritort

Publications and source records attributed to Felix Ritort.

At least 55 records · Page 3Linked to original sources

arXiv2009

Measurement of work in single-molecule experiments

A main goal of single-molecule experiments is to evaluate equilibrium free energy differences by applying fluctuation relations to repeated work measurements along irreversible processes. We quantify the error that is made in a free energy estimate by means of the Jarzynski equality when the accumulated work expended on the whole system (including the instrument) is erroneously replaced by the work transferred to the subsystem consisting of the sole molecular construct. We find that the error may be as large as 100%, depending on the number of experiments and on the bandwidth of the data acquisition apparatus. Our theoretical estimate is validated by numerical simulations and pulling experiments on DNA hairpins using optical tweezers.

cond-mat.stat-mech↗

arXiv2009

Investigating the thermodynamics of small biosystems with optical tweezers

We present two examples of how single-molecule experimental techniques applied to biological systems can give insight into problems within the scope of equilibrium and nonequilibrium mesoscopic thermodynamics. The first example is the mapping of the free energy landscape of a macromolecule, the second the experimental verification of Crooks' fluctuation theorem. In both cases the experimental setup comprises optical tweezers and DNA molecules.

cond-mat.mes-hall↗

arXiv2009

Dynamic force spectroscopy of DNA hairpins. I. Force kinetics and free energy landscapes

We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force dependent Kramers-Bell rates. To test the theory we have designed a specific DNA hairpin sequence that shows two-state cooperative folding under mechanical tension and carried out pulling experiments using optical tweezers. We show how we can determine the parameters that characterize the molecular free energy landscape of such sequence from rupture force kinetic studies. Finally we combine such kinetic studies with experimental investigations of the Crooks fluctuation relation to derive the free energy of formation of the hairpin at zero force.

cond-mat.stat-mech↗

arXiv2009

Dynamic force spectroscopy of DNA hairpins. II. Irreversibility and dissipation

We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average dissipated work and the average hopping number in two state systems. It is shown how these quantities only depend on two parameters that characterize the folding/unfolding kinetics of the molecule: the fragility and the coexistence hopping rate. The latter has to be rescaled to take into account the appropriate experimental setup. Finally we carry out pulling experiments with optical tweezers in a specifically designed DNA hairpin that shows two-state cooperative folding. We then use these experimental results to validate our theoretical predictions.

cond-mat.stat-mech↗

arXiv2009

Recovery of free energy branches in single molecule experiments

We present a method for determining the free energy of coexisting states from irreversible work measurements. Our approach is based on a fluctuation relation that is valid for dissipative transformations in partially equilibrated systems. To illustrate the validity and usefulness of the approach, we use optical tweezers to determine the free energy branches of the native and unfolded states of a two-state molecule as a function of the pulling control parameter. We determine, within 0.6 kT accuracy, the transition point where the free energies of the native and the unfolded states are equal.

cond-mat.soft↗

arXiv2008

Single-domain protein folding: a multi-faceted problem

We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape approach. As far as experiments are concerned, we focus on the recent development of single-molecule techniques. In particular, we compare the results obtained with two main techniques: single protein force measurements with optical tweezers and single-molecule fluorescence in studies on the same protein (RNase H). This allows us to point out some controversial issues such as the nature of the denatured and intermediate states and possible folding pathways. After reviewing the various numerical simulation techniques, we show that on-lattice protein-like models can help to understand many controversial issues.

physics.bio-ph↗

arXiv2008

Unstructured intermediate states in single protein force experiments

Recent single-molecule force measurements on single-domain proteins have highlighted a three-state folding mechanism where a stabilized intermediate state (I) is observed on the folding trajectory between the stretched state and the native state. Here we investigate on-lattice protein-like heteropolymer models that lead to a three-state mechanism and show that force experiments can be useful to determine the structure of I. We have mostly found that I is composed of a core stabilized by a high number of native contacts, plus an unstructured extended chain. The lifetime of I is shown to be sensitive to modifications of the protein that spoil the core. We then propose three types of modifications--point mutations, cuts, and circular permutations--aiming at: (1) confirming the presence of the core and (2) determining its location, within one amino acid accuracy, along the polypeptide chain. We also propose force jump protocols aiming to probe the on/off-pathway nature of I.

physics.bio-ph↗

arXiv2007

Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise

The Jarzynski equality and the fluctuation theorem relate equilibrium free energy differences to non-equilibrium measurements of the work. These relations extend to single-molecule experiments that have probed the finite-time thermodynamics of proteins and nucleic acids. The effects of experimental error and instrument noise have not previously been considered. Here, we present a Bayesian formalism for estimating free-energy changes from non-equilibrium work measurements that compensates for instrument noise and combines data from multiple driving protocols. We reanalyze a recent set of experiments in which a single RNA hairpin is unfolded and refolded using optical tweezers at three different rates. Interestingly, the fastest and farthest-from-equilibrium measurements contain the least instrumental noise, and therefore provide a more accurate estimate of the free energies than a few slow, more noisy, near-equilibrium measurements. The methods we propose here will extend the scope of single-molecule experiments; they can be used in the analysis of data from measurements with AFM, optical, and magnetic tweezers.

cond-mat.stat-mech↗

arXiv2004

Dynamical AC study of the critical behavior in Heisenberg spin glasses

We present some numerical results for the Heisenberg spin-glass model with Gaussian interactions, in a three dimensional cubic lattice. We measure the AC susceptibility as a function of temperature and determine an apparent finite temperature transition which is compatible with the chiral-glass temperature transition for this model. The relaxation time diverges like a power law $τ\sim (T-T_c)^{-zν}$ with $T_c=0.19(4)$ and $zν=5.0(5)$. Although our data indicates that the spin-glass transition occurs at the same temperature as the chiral glass transition, we cannot exclude the possibility of a chiral-spin coupling scenario for the lowest frequencies investigated.

cond-mat.other↗

arXiv2004

Thermodynamic and kinetic aspects of RNA pulling experiments

Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected to two polymers (handles) and a bead, trapped in the optical potential, attached to one of the handles. Initially, we focus on small single-domain RNA molecules which unfold in a cooperative way. The model qualitatively reproduces the experimental results and allow us to investigate the influence of the bead and handles on the unfolding reaction. A main ingredient of our model is to consider the appropriate statistical ensemble and the corresponding thermodynamic potential describing thermal fluctuations in the system. We then investigate several questions relevant to extract thermodynamic information from the experimental data. Next, we study the kinetics using a dynamical model. Finally, we address the more general problem of a multidomain RNA molecule with Mg2+-tertiary contacts that unfolds in a sequential way and propose techniques to analyze the breakage force data in order to obtain the reliable kinetics parameters that characterize each domain.

cond-mat.stat-mech↗

arXiv2003

Order-parameter fluctuations in Ising spin glasses at low temperatures

We present a numerical study of the order-parameter fluctuations for Ising spin glasses in three and four dimensions at very low temperatures and without an external field. Accurate measurements of two previously introduced parameters, A and G, show that the order parameter is not self-averaging, consistent with a zero-temperature thermal exponent value θ' \simeq 0, and confirm the validity of the relation G=1/3 in the thermodynamic limit in the whole low-temperature phase, as predicted by stochastic stability arguments.

cond-mat.dis-nn↗

arXiv2003

Frequency-domain study of $α$-relaxation in the Random Orthogonal Model

The time-dependent susceptibility for the finite-size mean-field Random Orthogonal model (ROM) is studied numerically for temperatures above the mode-coupling temperature. The results show that the imaginary part of the susceptibility $χ''(ν)$ obeys the scaling form proposed for glass-forming liquids with the peak frequency decreasesing as the temperature is lowered consistently with the Vogel-Fulcher law with a critical temperature remarkably close to the known critical temperature $T_c$ of the model where the configurational entropy vanishes.

cond-mat.dis-nn↗

arXiv2003

Glassy dynamics of kinetically constrained models

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, aging 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.

cond-mat.stat-mech↗

arXiv2002

Temperature shifts in the Sinai model: static and dynamical effects

We study analytically and numerically the role of temperature shifts in the simplest model where the energy landscape is explicitely hierarchical, namely the Sinai model. This model has both attractive features (there are valleys within valleys in a strict self similar sense), but also one important drawback: there is no phase transition so that the model is, in the large size limit, effectively at zero temperature. We compute various static chaos indicators, that are found to be trivial in the large size limit, but exhibit interesting features for finite sizes. Correspondingly, for finite times, some interesting rejuvenation effects, related to the self similar nature of the potential, are observed. Still, the separation of time scales/length scales with temperatures in this model is much weaker that in experimental spin-glasses.

cond-mat.dis-nn↗

arXiv2001

A real-space description of the glass transition based on heterogeneities and entropy barriers

An alternative scenario for the glass transition based on the cooperative nature of nucleation processes and the role of entropic effects is presented. The new ingredient is to relate the dissipation during the relaxation process to the release of strain energy driven by the nucleation of progressively larger cooperative spatial regions. Using an equiprobability hypothesis for the transition between different metastable configurations, we obtain a relation between the free energy dissipation rate and the size of the largest cooperative regions. Th is leads to a new phenomenological relation between the largest relaxation time in the supercooled liquid phase and the effective temperature. This differs from the classical Adam-Gibbs relation in that predicts no divergence of the primary relaxation time at the Kauzmann temperature but a crossover from fragile to strong behavior.

cond-mat.stat-mech↗

arXiv2001

Scaling approach to order-parameter fluctuations in disordered frustrated systems

We present a constructive approach to obtain information about the compactness and shape of large-scale lowest excitations in disordered systems by studying order-parameter fluctuations (OPF) at low temperatures. We show that the parameter $G$ which measures OPF is 1/3 at T=0 provided the ground state is unique and the probability distribution for the lowest excitations is gapless and with finite weight at zero-excitation energy. We then apply zero-temperature scaling to describe the energy and volume spectra of the lowest large-scale excitations which scale with the system size and have a weight at ze ro energy $\hat{P}_v(0)\sim l^{-θ'}$ with $v=l^d$. A low-temperature expansion reveals that, OPF vanish like $L^{-θ}$, if $θ> 0$ and remain finite for space filling lowest excitations with $θ=0$. The method can be extended to extract information about the shape and fractal surface of the large-scale lowest excitations.

cond-mat.stat-mech↗

arXiv2001

Strong Soret effect in one dimension

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.

cond-mat.stat-mech↗

arXiv2001

Validity of the zero-thermodynamic law in off-equilibrium coupled harmonic oscillators

In order to describe the thermodynamics of the glassy systems it has been recently introduced an extra parameter also called effective temperature which generalizes the fluctuation-dissipation theorem (FDT) to systems off-equilibrium and supposedly describes thermal fluctuations around the aging state. Here we investigate the applicability of a zero-th law for non-equilibrium glassy systems based on these effective temperatures by studying two coupled subsystems 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 two interacting subsystems coincide, 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.

cond-mat.dis-nn↗