Aging phenomena in nonlinear dissipative chains: Application to polymer

We study energy relaxation in a phenomenological model for polymer built from rheological considerations: a one dimensional nonlinear lattice with dissipative couplings. These couplings are well known in polymer's community to be possibly responsible of beta-relaxation (as in Burger's model). After thermalisation of this system, the extremities of the chain are put in contact with a zero-temperature reservoir, showing the existence of surprising quasi-stationary states with non zero energy when the dissipative coupling is high. This strange behavior, due to long-lived nonlinear localized modes, induces stretched exponential laws. Furthermore, we observe a strong dependence on the waiting time tw after the quench of the two-time intermediate correlation function C(tw+t,tw). This function can be scaled onto a master curve, similar to the case of spin or Lennard-Jones glasses.Comment: 8 pages, 10 figure

Disorder and fluctuations in nonlinear excitations in DNA

We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic potentials, [F. Dom\'\i nguez-Adame {\em et al.}, Phys. Rev. E {\bf 52}, 2183 (1995)], we analyze the behavior of lattices built from real DNA sequences obtained from human genome data. We confirm the existence of threshold forces, already found in Fibonacci sequences, and of stop positions highly dependent on the specific sequence. Another relevant conclusion is that the effective potential, a collective coordinate formalism introduced by Salerno and Kivshar [Phys. Lett. A {\bf 193}, 263 (1994)] is a useful tool to identify key regions that control the behaviour of a larger sequence. We then study how the fluctuations can assist the propagation process by helping the excitations to escape the stop positions. Our conclusions point out to improvements of the model which look promising to describe mechanical denaturation of DNA. Finally, we also consider how randomly distributed energy focus on the chain as a function of the sequence.Comment: 14 pages, final version, accepted in Fluctuation and Noise Letters, scheduled to apper in vol. 4, issue 3 (2004

Discrete Breathers in a Realistic Coarse-Grained Model of Proteins

We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. In the case of the small $\beta$-barrel structure that we consider, localization occurs on the turns connecting the strands. At high energies, discrete breathers stabilize the structure by concentrating energy on few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of this two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.Comment: Submitted to Physical Biolog

Breathers in oscillator chains with Hertzian interactions

We prove nonexistence of breathers (spatially localized and time-periodic oscillations) for a class of Fermi-Pasta-Ulam lattices representing an uncompressed chain of beads interacting via Hertz's contact forces. We then consider the setting in which an additional on-site potential is present, motivated by the Newton's cradle under the effect of gravity. Using both direct numerical computations and a simplified asymptotic model of the oscillator chain, the so-called discrete p-Schr\"odinger (DpS) equation, we show the existence of discrete breathers and study their spectral properties and mobility. Due to the fully nonlinear character of Hertzian interactions, breathers are found to be much more localized than in classical nonlinear lattices and their motion occurs with less dispersion. In addition, we study numerically the excitation of a traveling breather after an impact at one end of a semi-infinite chain. This case is well described by the DpS equation when local oscillations are faster than binary collisions, a situation occuring e.g. in chains of stiff cantilevers decorated by spherical beads. When a hard anharmonic part is added to the local potential, a new type of traveling breather emerges, showing spontaneous direction-reversing in a spatially homogeneous system. Finally, the interaction of a moving breather with a point defect is also considered in the cradle system. Almost total breather reflections are observed at sufficiently high defect sizes, suggesting potential applications of such systems as shock wave reflectors

Discrete localized modes supported by an inhomogeneous defocusing nonlinearity

We report that infinite and semi-infinite lattices with spatially inhomogeneous self-defocusing (SDF)\ onsite nonlinearity, whose strength increases rapidly enough toward the lattice periphery, support stable unstaggered (UnST) discrete bright solitons, which do not exist in lattices with the spatially uniform SDF nonlinearity. The UnST solitons coexist with stable staggered (ST) localized modes, which are always possible under the defocusing onsite nonlinearity. The results are obtained in a numerical form, and also by means of variational approximation (VA). In the semi-infinite (truncated) system, some solutions for the UnST surface solitons are produced in an exact form. On the contrary to surface discrete solitons in uniform truncated lattices, the threshold value of the norm vanishes for the UnST solitons in the present system. Stability regions for the novel UnST solitons are identified. The same results imply the existence of ST discrete solitons in lattices with the spatially growing self-focusing nonlinearity, where such solitons cannot exist either if the nonlinearity is homogeneous. In addition, a lattice with the uniform onsite SDF nonlinearity and exponentially decaying inter-site coupling is introduced and briefly considered too. Via a similar mechanism, it may also support UnST discrete solitons, under the action of the SDF nonlinearity. The results may be realized in arrayed optical waveguides and collisionally inhomogeneous Bose-Einstein condensates trapped in deep optical lattices. A generalization for a two-dimensional system is briefly considered too.Comment: 14 pages, 7 figures, accepted for publication in PR

Nonlinear waves in Newton's cradle and the discrete p-Schroedinger equation

We study nonlinear waves in Newton's cradle, a classical mechanical system consisting of a chain of beads attached to linear pendula and interacting nonlinearly via Hertz's contact forces. We formally derive a spatially discrete modulation equation, for small amplitude nonlinear waves consisting of slow modulations of time-periodic linear oscillations. The fully-nonlinear and unilateral interactions between beads yield a nonstandard modulation equation that we call the discrete p-Schroedinger (DpS) equation. It consists of a spatial discretization of a generalized Schroedinger equation with p-Laplacian, with fractional p>2 depending on the exponent of Hertz's contact force. We show that the DpS equation admits explicit periodic travelling wave solutions, and numerically find a plethora of standing wave solutions given by the orbits of a discrete map, in particular spatially localized breather solutions. Using a modified Lyapunov-Schmidt technique, we prove the existence of exact periodic travelling waves in the chain of beads, close to the small amplitude modulated waves given by the DpS equation. Using numerical simulations, we show that the DpS equation captures several other important features of the dynamics in the weakly nonlinear regime, namely modulational instabilities, the existence of static and travelling breathers, and repulsive or attractive interactions of these localized structures