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Michel Peyrard

Publications and source records attributed to Michel Peyrard.

At least 19 recordsLinked to original sources
arXiv2026

Probing the statistics of sequence-dependent DNA conformations in solution using SAXS

SAXS studies of four 60 base-pair DNA duplexes with sequences closely related to part of the GAGE6 (G-antigen 6) promoter have been performed to study the role of DNA conformations in solution and their potential relationship to DNA-protein binding. We show that the SAXS data can be analysed using a simple polymer model which nevertheless quantitatively describes the average persistence length and torsional rigidity of the DNA double helix to determine the statistical distribution of local conformations of the DNA in solution to a high accuracy. Although the SAXS data is averaged over time and all spatial orientations of the molecules, for sequences which have some asymmetry in the data we show that the conformations can be oriented with respect to the sequence. This allows specific features detected by the analysis to be precisely related to the DNA sequence, opening up new opportunities for SAXS to investigate the properties of DNA in solution. The biological implications of these results are discussed.

physics.bio-ph↗
arXiv2023

What can we learn from the dynamics of the Covid-19 epidemic ?

We investigate the mechanisms behind the quasi-periodic outbursts on the Covid-19 epidemics. Data for France and Germany show that the patterns of outbursts exhibit a qualitative change in early 2022, which appears in a change in their average period, and which is confirmed by time-frequency analysis. This provides a signal which can be used to discriminate among several mechanisms. Two main ideas have been proposed to explain periodicity in epidemics. One involves memory effects and another considers exchanges between epidemic clusters and a reservoir of population. We test these two approaches in the particular case of the Covid-19 epidemics and show that the "cluster model" is the only one which appears to be able to explain the observed pattern with realistic parameters. A last section discusses our results in the context of early studies of epidemics, and we stress the importance to work with models with a limited number of parameters, which moreover can be sufficiently well estimated, to draw conclusions on the general mechanisms behind the observations.

q-bio.PE↗
arXiv2022

Understanding temperature modulated calorimetry through studies of a model system

Temperature Modulated calorimetry is widely used but still raises some fundamental questions. In this paper we study a model system as a test sample to address some of them. The model has a nontrivial spectrum of relaxation times. We investigate temperature modulated calorimetry at constant average temperature to precise the meaning of the frequency-dependent heat capacity, its relation with entropy production, and how such measurements can observe the aging of a glassy sample leading to a time-dependent heat capacity. The study of the Kovacs effect for an out-of-equilibrium system shows how temperature modulated calorimetry could contribute to the understanding of this memory effect. Then we compare measurements of standard scanning calorimetry and temperature-modulated calorimetry and show how the two methods are complementary because they do not observe the same features. While it can probe the time scales of energy transfers in a system, even in the limit of low frequency temperature modulated calorimetry does not probe some relaxation phenomena which can be measured by scanning calorimetry, as suggested by experiments with glasses.

cond-mat.stat-mech↗
arXiv2020

Memory effects in glasses: insights into the thermodynamics of out of equilibrium systems revealed by a simple model of the Kovacs effect

This paper is an extended version of an article accepted for publication in Physical Review E. Besides its fundamental interest, the model that we investigate in this article is simple enough to be used as a basis for courses or tutorials on the thermodynamics of out of equilibrium systems. It allows simple numerical calculations and analytical analysis which highlight important concepts with an easily workable example. This version includes studies of fast cooling and heating, exhibiting cases with negative heat capacity, and further discussions on the entropy which are not presented in the Physical Review E version. Glasses are interesting materials because they allow us to explore the puzzling properties of out-of-equilibrium systems. One of them is the Kovacs effect in which a glass, brought to an out-of-equilibrium state in which all its thermodynamic variables are identical to those of an equilibrium state, nevertheless evolves, showing a hump in some global variable before the thermodynamic variables come back to their starting point. We show that a simple three-state system is sufficient to study this phenomenon using numerical integrations and exact analytical calculations. It also brings some light on the concept of fictive temperature, often used to extend standard thermodynamics to the out-of-equilibrium properties of glasses. We confirm that the concept of a unique fictive temperature is not valid, an show it can be extended to make a connection with the various relaxation processes in the system. The model also brings further insights on the thermodynamics of out-of-equilibrium systems. Moreover we show that the three-state model is able to describe various effects observed in glasses such as the asymmetric relaxation to equilibrium discussed by Kovacs, or the reverse crossover measured on $B_2O_3$.

cond-mat.stat-mech↗
arXiv2020

How is information transmitted in a nerve?

In the last fifteen years a debate emerged about the validity of the famous Hodgkin-Huxley model for nerve impulse. Mechanical models have been proposed. This note reviews the experimental properties of the nerve impulse and discusses the proposed alternatives. The experimental data, which rule out some of the alternative suggestions, show that, while the Hodgkin-Huxley model may not be complete, it nevertheless includes essential features that should not be overlooked in the attempts made to improve, or supersede, it.

physics.bio-ph↗
arXiv2020

Onset of sliding of elastomer multicontacts: failure of a model of independent asperities to match experiments

Modelling of rough frictional interfaces is often based on asperity models, in which the individual behaviour of individual microjunctions is assumed. In the absence of local measurements at the microjunction scale, quantitative comparison of such models with experiments is usually based only on macroscopic quantities, like the total tangential load resisted by the interface. Recently however, a new experimental dataset was presented on the onset of sliding of rough elastomeric interfaces, which includes local measurements of the contact area of the individual microjunctions. Here, we use this more comprehensive dataset to test the possibility of quantitatively matching the measurements with a model of independent asperities, enriched with experimental information about the area of microjunctions and its evolution under shear. We show that, despite using parameter values and behaviour laws constrained and inspired by experiments, our model does not quantitatively match the macroscopic measurements. We discuss the possible origins of this failure .

cond-mat.soft↗
arXiv2018

Kinky DNA in solution: Small angle scattering study of a nucleosome positioning sequence

DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$Å is inconsistent with recent studies on short-chain DNA that show much greater flexibility but do not probe its origin. We have performed X-ray and neutron small-angle scattering on a short DNA sequence containing a strong nucleosome positioning element, and analyzed the results using a modified Kratky-Porod model to determine possible conformations. Our results support a hypothesis from Crick and Klug in 1975 that some DNA sequences in solution can have sharp kinks, potentially resolving the discrepancy. Our conclusions are supported by measurements on a radiation-damaged sample, where single-strand breaks lead to increased flexibility and by an analysis of data from another sequence, which does not have kinks, but where our method can detect a locally enhanced flexibility due to an $AT$-domain.

physics.bio-ph↗
arXiv2015

From thermal rectifiers to thermoelectric devices

We discuss thermal rectification and thermoelectric energy conversion from the perspective of nonequilibrium statistical mechanics and dynamical systems theory. After preliminary considerations on the dynamical foundations of the phenomenological Fourier law in classical and quantum mechanics, we illustrate ways to control the phononic heat flow and design thermal diodes. Finally, we consider the coupled transport of heat and charge and discuss several general mechanisms for optimizing the figure of merit of thermoelectric efficiency.

cond-mat.stat-mech↗
arXiv2014

Characterization of the low temperature properties of a simplified protein model

Prompted by results that showed that a simple protein model, the frustrated Gō model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature properties of proteins. First, we examine equilibrium fluctuations. We calculate its incoherent neutron-scattering structure factor and show that it can be well described by a theory using the one-phonon approximation. By performing an inherent structure analysis, we assess the transitions among energy states at low temperatures. Then, we examine non-equilibrium fluctuations after a sudden cooling of the protein. We investigate the violation of the fluctuation--dissipation theorem in order to analyze the protein glass transition. We find that the effective temperature of the quenched protein deviates from the temperature of the thermostat, however it relaxes towards the actual temperature with an Arrhenius behavior as the waiting time increases. These results of the equilibrium and non-equilibrium studies converge to the conclusion that the apparent dynamical transition of this coarse-grained model cannot be attributed to a glassy behavior.

cond-mat.stat-mech↗
arXiv2012

The dynamics of the DNA denaturation transition

The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate shows a minimum, but then increases as function of length. We also examine the influence of sequence and solvent friction. Molecules having the same number of weak and strong base-pairs can have significantly different opening rates depending on the order of base-pairs.

physics.bio-ph↗
arXiv2012

Base Pair Openings and Temperature Dependence of DNA Flexibility

The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot model with soft and hard joints, corresponding to open and closed base pairs, and sequence-dependent statistical information about the state of each pair provided by a Peyrard-Bishop-Dauxois (PBD) model calculation with no freely adjustable parameters.

cond-mat.stat-mech↗
arXiv2012

Collective effects at frictional interfaces

We discuss the role of the long-range elastic interaction between the contacts inside an inhomogeneous frictional interface. The interaction produces a characteristic elastic correlation length $λ_c = a^2 E / k_c$ (where $a$ is the distance between the contacts, $k_c$ is the elastic constant of a contact, and $E$ is the Young modulus of the sliding body), below which the slider may be considered as a rigid body. The strong inter-contact interaction leads to a narrowing of the effective threshold distribution for contact breaking and enhances the chances for an elastic instability to appear. Above the correlation length, $r > λ_c$, the interaction leads to screening of local perturbations in the interface, or to appearance of collective modes --- frictional cracks propagating as solitary waves.

cond-mat.stat-mech↗
arXiv2011

Structural correlations and melting of B-DNA fibres

Despite numerous attempts, the understanding of the thermal denaturation of DNA is still a challenge due to the lack of structural data at the transition since standard experimental approaches to DNA melting are made in solution and do not provide spatial information. We report a measurement using neutron scattering from oriented DNA fibres to determine the size of the regions that stay in the double-helix conformation as the melting temperature is approached from below. A Bragg peak from the B-form of DNA has been observed as a function of temperature and its width and integrated intensity have bean measured. These results, complemented by a differential calorimetry study of the melting of B DNA fibres as well as electrophoresis and optical observation data, are analysed in terms of a one-dimensional mesoscopic model of DNA.

cond-mat.stat-mech↗
arXiv2011

Dependence of kinetic friction on velocity: Master equation approach

We investigate the velocity dependence of kinetic friction with a model which makes minimal assumptions on the actual mechanism of friction so that it can be applied at many scales provided the system involves multi-contact friction. Using a recently developed master equation approach we investigate the influence of two concurrent processes. First, at a nonzero temperature thermal fluctuations allow an activated breaking of contacts which are still below the threshold. As a result, the friction force monotonically increases with velocity. Second, the aging of contacts leads to a decrease of the friction force with velocity. Aging effects include two aspects: the delay in contact formation and aging of a contact itself, i.e., the change of its characteristics with the duration of stationary contact. All these processes are considered simultaneously with the master equation approach, giving a complete dependence of the kinetic friction force on the driving velocity and system temperature, provided the interface parameters are known.

cond-mat.stat-mech↗
arXiv2011

The thermal denaturation of DNA studied with neutron scattering

The melting transition of deoxyribonucleic acid (DNA), whereby the strands of the double helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fibre DNA has been measured as a function of temperature, and its widths and integrated intensities have been interpreted using the Peyrard-Bishop-Dauxois (PBD) model with only one free parameter. The experiment is unique, as it gives spatial correlation along the molecule through the melting transition where other techniques cannot.

cond-mat.stat-mech↗
arXiv2010

Master equation approach to friction at the mesoscale

At the mesoscale friction occurs through the breaking and formation of local contacts. This is often described by the earthquake-like model which requires numerical studies. We show that this phenomenon can also be described by a master equation, which can be solved analytically in some cases and provides an efficient numerical solution for more general cases. We examine the effect of temperature and aging of the contacts and discuss the statistical properties of the contacts for different situations of friction and their implications, particularly regarding the existence of stick-slip.

cond-mat.stat-mech↗
arXiv2009

Critical examination of the inherent-structure-landscape analysis of two-state folding proteins

Recent studies attracted the attention on the inherent structure landscape (ISL) approach as a reduced description of proteins allowing to map their full thermodynamic properties. However, the analysis has been so far limited to a single topology of a two-state folding protein, and the simplifying assumptions of the method have not been examined. In this work, we construct the thermodynamics of four two-state folding proteins of different sizes and secondary structure by MD simulations using the ISL method, and critically examine possible limitations of the method. Our results show that the ISL approach correctly describes the thermodynamics function, such as the specific heat, on a qualitative level. Using both analytical and numerical methods, we show that some quantitative limitations cannot be overcome with enhanced sampling or the inclusion of harmonic corrections.

cond-mat.stat-mech↗