q-Breathers and the Fermi-Pasta-Ulam Problem

The Fermi-Pasta-Ulam (FPU) paradox consists of the nonequipartition of energy among normal modes of a weakly anharmonic atomic chain model. In the harmonic limit each normal mode corresponds to a periodic orbit in phase space and is characterized by its wave number $q$. We continue normal modes from the harmonic limit into the FPU parameter regime and obtain persistence of these periodic orbits, termed here $q$-Breathers (QB). They are characterized by time periodicity, exponential localization in the $q$-space of normal modes and linear stability up to a size-dependent threshold amplitude. Trajectories computed in the original FPU setting are perturbations around these exact QB solutions. The QB concept is applicable to other nonlinear lattices as well.Comment: 4 pages, 4 figure

Tail resonances of FPU q-breathers and their impact on the pathway to equipartition

Upon initial excitation of a few normal modes the energy distribution among all modes of a nonlinear atomic chain (the Fermi-Pasta-Ulam model) exhibits exponential localization on large time scales. At the same time resonant anomalies (peaks) are observed in its weakly excited tail for long times preceding equipartition. We observe a similar resonant tail structure also for exact time-periodic Lyapunov orbits, coined q-breathers due to their exponential localization in modal space. We give a simple explanation for this structure in terms of superharmonic resonances. The resonance analysis agrees very well with numerical results and has predictive power. We extend a previously developed perturbation method, based essentially on a Poincare-Lindstedt scheme, in order to account for these resonances, and in order to treat more general model cases, including truncated Toda potentials. Our results give qualitative and semiquantitative account for the superharmonic resonances of q-breathers and natural packets

Escorted Free Energy Simulations: Improving Convergence by Reducing Dissipation

Nonequilibrium, ``fast switching'' estimates of equilibrium free energy differences, Delta F, are often plagued by poor convergence due to dissipation. We propose a method to improve these estimates by generating trajectories with reduced dissipation. Introducing an artificial flow field that couples the system coordinates to the external parameter driving the simulation, we derive an identity for Delta F in terms of the resulting trajectories. When the flow field effectively escorts the system along a near-equilibrium path, the free energy estimate converges efficiently and accurately. We illustrate our method on a model system, and discuss the general applicability of our approach.Comment: 4 pages, including 2 figures, accepted for publication in Phys Rev Let

On the Spectrum of the Resonant Quantum Kicked Rotor

It is proven that none of the bands in the quasi-energy spectrum of the Quantum Kicked Rotor is flat at any primitive resonance of any order. Perturbative estimates of bandwidths at small kick strength are established for the case of primitive resonances of prime order. Different bands scale with different powers of the kick strength, due to degeneracies in the spectrum of the free rotor.Comment: Description of related published work has been expanded in the Introductio

Transport properties of one-dimensional Kronig-Penney models with correlated disorder

Transport properties of one-dimensional Kronig-Penney models with binary correlated disorder are analyzed using an approach based on classical Hamiltonian maps. In this method, extended states correspond to bound trajectories in the phase space of a parametrically excited linear oscillator, while the on site-potential of the original model is transformed to an external force. We show that in this representation the two probe conductance takes a simple geometrical form in terms of evolution areas in phase-space. We also analyze the case of a general N-mer model.Comment: 16 pages in Latex, 12 Postscript figures include

Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations

Formation of bacteriorhodopsin (bR) from apoprotein and retinal has been studied experimentally, but the actual pathway, including the point of entry, is little understood. Molecular dynamics simulations provide a surprisingly clear prediction. A window between bR helices E and F in the transmembrane part of the protein can be identified as an entry point for retinal. Steered molecular dynamics, performed by applying a series of external forces in the range of 200–1000 pN over a period of 0.2 ns to retinal, allows one to extract this chromophore from bR once the Schiff base bond to Lys216 is cleaved. Extraction proceeds until the retinal tail forms a hydrogen bond network with Ala144, Met145, and Ser183 side groups lining the exit/entry window. The manipulation induces a distortion with a fitted root mean square deviation of coordinates (ignoring retinal, water, and hydrogen atoms) of less than 1.9 A by the time the retinal carbonyl reaches the protein surface. The forces needed to extract retinal are due to friction and do not indicate significant potential barriers. The simulations therefore suggest a pathway for the binding of retinal. Water molecules are found to play a crucial role in the binding process

Onset of Delocalization in Quasi-1D Waveguides with Correlated Surface Disorder

We present first analytical results on transport properties of many-mode waveguides with rough surfaces having long-range correlations. We show that propagation of waves through such waveguides reveals a quite unexpected phenomena of a complete transparency for a subset of propagating modes. These modes do not interact with each other and effectively can be described by the theory of 1D transport with correlated disorder. We also found that with a proper choice of model parameters one can arrange a perfect transparency of waveguides inside a given window of energy of incoming waves. The results may be important in view of experimental realizations of a selective transport in application to both waveguides and electron/optic nanodevices.Comment: RevTex, 4 pages, no figures, few references are adde

Signum Function Method for Generation of Correlated Dichotomic Chains

We analyze the signum-generation method for creating random dichotomic sequences with prescribed correlation properties. The method is based on a binary mapping of the convolution of continuous random numbers with some function originated from the Fourier transform of a binary correlator. The goal of our study is to reveal conditions under which one can construct binary sequences with a given pair correlator. Our results can be used in the construction of superlattices and waveguides with selective transport properties.Comment: 14 pages, 7 figure

Mobility Edge in Aperiodic Kronig-Penney Potentials with Correlated Disorder: Perturbative Approach

It is shown that a non-periodic Kronig-Penney model exhibits mobility edges if the positions of the scatterers are correlated at long distances. An analytical expression for the energy-dependent localization length is derived for weak disorder in terms of the real-space correlators defining the structural disorder in these systems. We also present an algorithm to construct a non-periodic but correlated sequence exhibiting desired mobility edges. This result could be used to construct window filters in electronic, acoustic, or photonic non-periodic structures.Comment: RevTex, 4 pages including 2 Postscript figure