Stability criteria of the Vlasov equation and quasi-stationary states of the HMF model

We perform a detailed study of the relaxation towards equilibrium in the Hamiltonian Mean-Field (HMF) model, a prototype for long-range interactions in $N$-particle dynamics. In particular, we point out the role played by the infinity of stationary states of the associated $N ~$ Vlasov dynamics. In this context, we derive a new general criterion for the stability of any spatially homogeneous distribution, and compare its analytical predictions with numerical simulations of the Hamiltonian, finite $N$, dynamics. We then propose and verify numerically a scenario for the relaxation process, relying on the Vlasov equation. When starting from a non stationary or a Vlasov unstable stationary initial state, the system shows initially a rapid convergence towards a stable stationary state of the Vlasov equation via non stationary states: we characterize numerically this dynamical instability in the finite $N$ system by introducing appropriate indicators. This first step of the evolution towards Boltzmann-Gibbs equilibrium is followed by a slow quasi-stationary process, that proceeds through different stable stationary states of the Vlasov equation. If the finite $N$ system is initialized in a Vlasov stable homogenous state, it remains trapped in a quasi-stationary state for times that increase with the nontrivial power law $N^{1.7}$. Single particle momentum distributions in such a quasi-stationary regime do not have power-law tails, and hence cannot be fitted by the $q$-exponential distributions derived from Tsallis statistics.Comment: To appear in Physica

Ensemble inequivalence, bicritical points and azeotropy for generalized Fofonoff flows

We present a theoretical description for the equilibrium states of a large class of models of two-dimensional and geophysical flows, in arbitrary domains. We account for the existence of ensemble inequivalence and negative specific heat in those models, for the first time using explicit computations. We give exact theoretical computation of a criteria to determine phase transition location and type. Strikingly, this criteria does not depend on the model, but only on the domain geometry. We report the first example of bicritical points and second order azeotropy in the context of systems with long range interactions.Comment: 4 pages, submitted to Phys. Rev. Let

Topological Solitons and Folded Proteins

We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by assembling the solitons together, one after another. We present a simple theoretical model that realizes our proposal and apply it to a number of biologically active proteins including 1VII, 2RB8, 3EBX (Protein Data Bank codes). In all the examples that we have considered we are able to construct solitons that reproduce secondary structural motifs such as alpha-helix-loop-alpha-helix and beta-sheet-loop-beta-sheet with an overall root-mean-square-distance accuracy of around 0.7 Angstrom or less for the central alpha-carbons, i.e. within the limits of current experimental accuracy.Comment: 4 pages, 4 figure

Tensor products and statistics

AbstractA dictionary between operator-based and matrix-based languages in multivariate statistical analysis is proposed. Then this formulary is applied to asymptotic factorial analyses, especially for giving asymptotic covariance matrices and operators in an explicit form. Finally, we present the mathematical foundations on which are based the functional tools, i.e. tensor products of linear spaces, of vectors, and of operators

Lyapunov exponents as a dynamical indicator of a phase transition

We study analytically the behavior of the largest Lyapunov exponent $\lambda_1$ for a one-dimensional chain of coupled nonlinear oscillators, by combining the transfer integral method and a Riemannian geometry approach. We apply the results to a simple model, proposed for the DNA denaturation, which emphasizes a first order-like or second order phase transition depending on the ratio of two length scales: this is an excellent model to characterize $\lambda_1$ as a dynamical indicator close to a phase transition.Comment: 8 Pages, 3 Figure

Algebraic Correlation Function and Anomalous Diffusion in the HMF model

In the quasi-stationary states of the Hamiltonian Mean-Field model, we numerically compute correlation functions of momenta and diffusion of angles with homogeneous initial conditions. This is an example, in a N-body Hamiltonian system, of anomalous transport properties characterized by non exponential relaxations and long-range temporal correlations. Kinetic theory predicts a striking transition between weak anomalous diffusion and strong anomalous diffusion. The numerical results are in excellent agreement with the quantitative predictions of the anomalous transport exponents. Noteworthy, also at statistical equilibrium, the system exhibits long-range temporal correlations: the correlation function is inversely proportional to time with a logarithmic correction instead of the usually expected exponential decay, leading to weak anomalous transport properties

1-d gravity in infinite point distributions

The dynamics of infinite, asymptotically uniform, distributions of self-gravitating particles in one spatial dimension provides a simple toy model for the analogous three dimensional problem. We focus here on a limitation of such models as treated so far in the literature: the force, as it has been specified, is well defined in infinite point distributions only if there is a centre of symmetry (i.e. the definition requires explicitly the breaking of statistical translational invariance). The problem arises because naive background subtraction (due to expansion, or by "Jeans' swindle" for the static case), applied as in three dimensions, leaves an unregulated contribution to the force due to surface mass fluctuations. Following a discussion by Kiessling, we show that the problem may be resolved by defining the force in infinite point distributions as the limit of an exponentially screened pair interaction. We show that this prescription gives a well defined (finite) force acting on particles in a class of perturbed infinite lattices, which are the point processes relevant to cosmological N-body simulations. For identical particles the dynamics of the simplest toy model is equivalent to that of an infinite set of points with inverted harmonic oscillator potentials which bounce elastically when they collide. We discuss previous results in the literature, and present new results for the specific case of this simplest (static) model starting from "shuffled lattice" initial conditions. These show qualitative properties (notably its "self-similarity") of the evolution very similar to those in the analogous simulations in three dimensions, which in turn resemble those in the expanding universe.Comment: 20 pages, 8 figures, small changes (section II shortened, added discussion in section IV), matches final version to appear in PR

Two-Color Coherent Photodissociation of Nitrogen Oxide in Intense Laser Fields

A simple one-dimensional semi-classical model with a Morse potential is used to investigate the possibility of two-color infrared multi-photon dissociation of vibrationally excited nitrogen oxide. The amplitude ratio effects and adiabatic effects are investigated. Some initial states are found to have thresholds smaller than expected from single-mode considerations and multiple thresholds exist for initial states up to 32. PACS: 42.50.HzComment: 3 pages, old papers, add source files to replace original postscrip

Breather trapping and breather transmission in a DNA model with an interface

We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are oriented in opposite directions. The Hamiltonian of the Peyrard--Bishop model is augmented with a term that includes the dipole--dipole coupling between base pairs. Numerical simulations show the existence of two dynamical regimes. If the translational kinetic energy of a moving breather launched towards the interface is below a critical value, it is trapped in a region around the interface collecting vibrational energy. For an energy larger than the critical value, the breather is transmitted and continues travelling along the double strand with lower velocity. Reflection phenomena never occur. The same study has been carried out when a single dipole is oriented in opposite direction to the other ones. When moving breathers collide with the single inverted dipole, the same effects appear. These results emphasize the importance of this simple type of local inhomogeneity as it creates a mechanism for the trapping of energy. Finally, the simulations show that, under favorable conditions, several launched moving breathers can be trapped successively at the interface region producing an accumulation of vibrational energy. Moreover, an additional colliding moving breather can produce a saturation of energy and a moving breather with all the accumulated energy is transmitted to the chain.Comment: 15 pages, 11 figure