Biomedical subjects

Michel Peyrard

Publications and source records attributed to Michel Peyrard.

7 recordsLinked to original sources

PubMed2006

Modeling protein thermodynamics and fluctuations at the mesoscale.

We use an extended Go model, in unfrustrated and frustrated variants, to study the energy landscape and the fluctuations of a model protein. The model exhibits two transitions, folding and dynamical transitions, when changing the temperature. The inherent structures corresponding to the minima of the landscape are analyzed and we show how their energy density can be obtained from simulations around the folding temperature. The scaling of this energy density is found to reflect the folding transition. Moreover, this approach allows us to build a reduced thermodynamics in the inherent structure landscape. Equilibrium studies, from full molecular dynamics (MD) simulations and from the reduced thermodynamics, detect the features of a dynamical transition at low temperature and we analyze the location and time scale of the fluctuations of the protein, showing the need of some frustration in the model to get realistic results. The frustrated model also shows the presence of a kinetic trap which strongly affects the dynamics of folding.

Computer Simulation↗

PubMed2006

The inherent structure landscape of a protein.

Using the Gō model of a real protein, we explore the landscape of its metastable structures. First, we show how the inherent structure energy density can be obtained from the probability density determined by sampling molecular dynamics trajectories and quenching. The analysis of the inherent structure landscape can characterize the folding transition. Then we show how thermodynamics of the inherent states can be established to study the equilibrium properties of proteins. Our work brings some elements into the current discussion about the protein dynamical transition. The study uses a simplified model to illustrate the ideas, but, as the inherent structure landscape is much simpler than the free energy surface of the protein, it appears to be accessible for an all-atom model of a small protein, at the expense of much longer calculations.

Protein Conformation↗

PubMed2005

Can one predict DNA transcription start sites by studying bubbles?

It has been speculated that bubble formation of several base pairs due to thermal fluctuations is indicatory for biologically active sites. Recent evidence, based on experiments and molecular dynamics simulations using the Peyrard-Bishop-Dauxois model, seems to point in this direction. However, sufficiently large bubbles appear only seldom, which makes an accurate calculation difficult even for minimal models. In this Letter, we introduce a new method that is orders of magnitude faster than molecular dynamics. Using this method, we show that the present evidence is unsubstantiated.

DNA↗

PubMed2005

A model on the origin of RNA.

The theory of the liquid-glass transition is extended to describe the polymerization of RNA in a nucleotide-condensed state. In the glassy state the ribose subunits are joined by a 2'-5' or 3'-5' phosphodiester linkage to form the ribose-phosphate backbone similar to oligosaccharides and polysaccharides. The occurrence of the glass transition requires two conditions: (1) a supercooled state in a nucleotide-condensed state should exist below the temperature at which the whole RNA hydrolyzes; (2) the Gibbs free energy due to the Kauzmann entropy, which obeys a Curie law with a negative sign, must be larger than the height of the potential barrier for nucleotides to overcome to form the binding.

Models, Biological↗

PubMed2004

Nonlinear structures and thermodynamic instabilities in a one-dimensional lattice system.

The equilibrium states of the discrete Peyrard-Bishop Hamiltonian with one end fixed are computed exactly from the two-dimensional nonlinear Morse map. These exact nonlinear structures are interpreted as domain walls, interpolating between bound and unbound segments of the chain. Their free energy is calculated to leading order beyond the Gaussian approximation. Thermodynamic instabilities (e.g., DNA unzipping and/or thermal denaturation) can be understood in terms of domain wall formation.

Computer Simulation↗

PubMed2003

Thermal denaturation of a helicoidal DNA model.

We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e., the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal geometry of the molecule and allows an exact numerical evaluation of its thermodynamical properties. Dynamical simulations of long-enough molecular segments allow the study of the structure factors and of the properties of the denaturated regions. Simulations of finite chains display the hallmarks of a first order transition for sufficiently long-ranged stacking forces although a study of the model's "universality class" strongly suggests the presence of an "underlying" continuous transition.

Biophysical Phenomena↗

PubMed2003

One-dimensional "turbulence" in a discrete lattice.

We study a one-dimensional discrete analog of the von Karman flow, widely investigated in turbulence. A lattice of anharmonic oscillators is excited by both ends in order to create a large scale structure in a highly nonlinear medium, in the presence of a dissipative term proportional to the second order finite difference of the velocities, similar to the viscous term in a fluid. In a first part, the energy density is investigated in real and Fourier space in order to characterize the behavior of the system on a local scale. At low amplitude of excitation the large scale structure persists in the system but all modes are however excited and exchange energy, leading to a power law spectrum for the energy density, which is remarkably stable against changes in the model parameters, amplitude of excitation, or damping. In the spirit of shell models, this regime can be described in terms of interacting scales. At higher amplitude of excitation, the large scale structure is destroyed and the dynamics of the system can be viewed as resulting from the creation, interaction, and decay of localized excitations, the discrete breathers, the one-dimensional equivalents of vortices in a fluid. The spectrum of the energy density is well described by the spectrum of the breathers, and shows an exponential decay with the wave vector. Due to this exponential behavior, the spectrum is dominated by the most intense breathers. In this regime, the probability distribution of the increments of velocity between neighboring points is remarkably similar to the experimental results of turbulence and can be described by distributions deduced from nonextensive thermodynamics as in fluids. In a second part the power dissipated in the whole lattice is studied to characterize the global behavior of the system. Its probability distribution function shows non-Gaussian fluctuations similar to the one exhibited recently in a large class of "inertial systems," i.e., systems that cannot be divided into mesoscopic regions which are independent. The properties of the nonlinear excitations of the lattice provide a partial understanding of this behavior.

Journal Article↗