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We study the dynamical and chaotic behavior of a disordered one-dimensional elastic mechanical lattice, which supports translational and rotational waves. The model used in this work is motivated by the recent experimental results of Deng et al. [Nat. Commun. 9, 1 (2018)]. This lattice is characterized by strong geometrical nonlinearities and the coupling of two degrees-of-freedom (DoFs) per site. Although the linear limit of the structure consists of a linear Fermi-Pasta-Ulam-Tsingou lattice and a linear Klein-Gordon (KG) lattice whose DoFs are uncoupled, by using single site initial excitations on the rotational DoF, we evoke the nonlinear coupling between the system's translational and rotational DoFs. Our results reveal that such coupling induces rich wave-packet spreading behavior in the presence of strong disorder. In the weakly nonlinear regime, we observe energy spreading only due to the coupling of the two DoFs (per site), which is in contrast to what is known for KG lattices with a single DoF per lattice site, where the spreading occurs due to chaoticity. Additionally, for strong nonlinearities, we show that initially localized wave-packets attain near ballistic behavior in contrast to other known models. We also reveal persistent chaos during energy spreading, although its strength decreases in time as quantified by the evolution of the system's finite-time maximum Lyapunov exponent. Our results show that flexible, disordered, and strongly nonlinear lattices are a viable platform to study energy transport in combination with multiple DoFs (per site), also present an alternative way to control energy spreading in heterogeneous media.

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We present and validate simple and efficient methods to estimate the chaoticity of orbits in low-dimensional conservative dynamical systems, namely, autonomous Hamiltonian systems and area-preserving symplectic maps, from computations of Lagrangian descriptors (LDs) on short time scales. Two quantities are proposed for determining the chaotic or regular nature of orbits in a system's phase space, which are based on the values of the LDs of these orbits and of nearby ones: The difference and ratio of neighboring orbits' LDs. Using as generic test models the prototypical two degree of freedom Hénon-Heiles system and the two-dimensional standard map, we find that these indicators are able to correctly characterize the chaotic or regular nature of orbits to better than 90% agreement with results obtained by implementing the Smaller Alignment Index (SALI) method, which is a well-established chaos detection technique. Further investigating the performance of the two introduced quantities, we discuss the effects of the total integration time and of the spacing between the used neighboring orbits on the accuracy of the methods, finding that even typical short time, coarse-grid LD computations are sufficient to provide reliable quantification of the systems' chaotic component, using less CPU time than the SALI. In addition to quantifying chaos, the introduced indicators have the ability to reveal details about the systems' local and global chaotic phase space structure. Our findings clearly suggest that LDs can also be used to quantify and investigate chaos in continuous and discrete low-dimensional conservative dynamical systems.

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Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity in the framework of the Peyrard-Bishop-Dauxois model. Extensive microcanonical simulations are used with energies corresponding to physiological temperature. The bubble lifetime profiles along the DNA sequences demonstrate a significant reduction of the average lifetime at the mutation sites when the mutated promoter decreases transcription, while a corresponding enhancement of the bubble lifetime is observed in the case of mutations leading to increased transcription. The relative difference in bubble lifetimes between the mutated and wild type promoters at the position of mutation varies from 20% to more than 30% as the bubble length decreases.

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We study the chaotic dynamics of graphene structures, considering both a periodic, defect free, graphene sheet and graphene nanoribbons (GNRs) of various widths. By numerically calculating the maximum Lyapunov exponent, we quantify the chaoticity for a spectrum of energies in both systems. We find that for all cases, the chaotic strength increases with the energy density and that the onset of chaos in graphene is slow, becoming evident after more than 104 natural oscillations of the system. For the GNRs, we also investigate the impact of the width and chirality (armchair or zigzag edges) on their chaotic behavior. Our results suggest that due to the free edges, the chaoticity of GNRs is stronger than the periodic graphene sheet and decreases by increasing width, tending asymptotically to the bulk value. In addition, the chaotic strength of armchair GNRs is higher than a zigzag ribbon of the same width. Furthermore, we show that the composition of 12C and 13C carbon isotopes in graphene has a minor impact on its chaotic strength.

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We reveal the generic characteristics of wave-packet delocalization in two-dimensional nonlinear disordered lattices by performing extensive numerical simulations in two basic disordered models: the Klein-Gordon system and the discrete nonlinear Schrödinger equation. We find that in both models (a) the wave packet's second moment asymptotically evolves as t^{a_{m}} with a_{m}≈1/5 (1/3) for the weak (strong) chaos dynamical regime, in agreement with previous theoretical predictions [S. Flach, Chem. Phys. 375, 548 (2010)CMPHC20301-010410.1016/j.chemphys.2010.02.022]; (b) chaos persists, but its strength decreases in time t since the finite-time maximum Lyapunov exponent Λ decays as Λ∝t^{α_{Λ}}, with α_{Λ}≈-0.37 (-0.46) for the weak (strong) chaos case; and (c) the deviation vector distributions show the wandering of localized chaotic seeds in the lattice's excited part, which induces the wave packet's thermalization. We also propose a dimension-independent scaling between the wave packet's spreading and chaoticity, which allows the prediction of the obtained α_{Λ} values.

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We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version (ePBD) having a sequence-dependent stacking interaction, emphasizing the effect of the sequences' guanine-cytosine (GC)/adenine-thymine (AT) content on these distributions. For both models we find that base pair-dependent (GC vs AT) thresholds for considering complementary nucleotides to be separated are able to reproduce the observed dependence of the melting temperature on the GC content of the DNA sequence. Using these thresholds for base pair openings, we obtain bubble lifetime distributions for bubbles of lengths up to ten base pairs as the GC content of the sequences is varied, which are accurately fitted with stretched exponential functions. We find that for both models the average bubble lifetime decreases with increasing either the bubble length or the GC content. In addition, the obtained bubble length distributions are also fitted by appropriate stretched exponential functions and our results show that short bubbles have similar likelihoods for any GC content, but longer ones are substantially more likely to occur in AT-rich sequences. We also show that the ePBD model permits more, longer-lived, bubbles than the PBD system.

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We discuss the effect of heterogeneity on the chaotic properties of the Peyrard-Bishop-Dauxois nonlinear model of DNA. Results are presented for the maximum Lyapunov exponent and the deviation vector distribution. Different compositions of adenine-thymine (AT) and guanine-cytosine (GC) base pairs are examined for various energies up to the melting point of the corresponding sequence. We also consider the effect of the alternation index, which measures the heterogeneity of the DNA chain through the number of alternations between different types (AT or GC) of base pairs, on the chaotic behavior of the system. Biological gene promoter sequences have been also investigated, showing no distinct behavior of the maximum Lyapunov exponent.

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We numerically investigate the dynamics of strongly disordered 1D lattices under single-particle displacements, using both the Hertzian model, describing a granular chain, and the α+ß Fermi-Pasta-Ulam-Tsingou model (FPUT). The most profound difference between the two systems is the discontinuous nonlinearity of the granular chain appearing whenever neighboring particles are detached. We therefore sought to unravel the role of these discontinuities in the destruction of Anderson localization and their influence on the system's chaotic dynamics. Our results show that the dynamics of both models can be characterized by: (i) localization with no chaos; (ii) localization and chaos; (iii) spreading of energy, chaos, and equipartition. The discontinuous nonlinearity of the Hertzian model is found to trigger energy spreading at lower energies. More importantly, a transition from Anderson localization to energy equipartition is found for the Hertzian chain and is associated with the "propagation" of the discontinuous nonlinearity in the chain. On the contrary, the FPUT chain exhibits an alternate behavior between localized and delocalized chaotic behavior which is strongly dependent on the initial energy excitation.

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We investigate the dynamics of highly polydisperse finite granular chains. From the spatiospectral properties of small vibrations, we identify which particular single-particle displacements lead to energy localization. Then, we address a fundamental question: Do granular nonlinearities and the resulting chaotic dynamics destroy this energy localization? Our numerical simulations show that for moderate nonlinearities, the overall system behaves chaotically, and spreading of energy occurs. However, long-lasting chaotic energy localization is observed for particular single-particle excitations in the presence of the nonsmooth nonlinearities. On the other hand, for sufficiently strong nonlinearities, the granular chain reaches energy equipartition. In this case, an equilibrium chaotic state is reached independent of the initial position excitation.

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We investigate the energy transport in one-dimensional disordered granular solids by extensive numerical simulations. In particular, we consider the case of a polydisperse granular chain composed of spherical beads of the same material and with radii taken from a random distribution. We start by examining the linear case, in which it is known that the energy transport strongly depends on the type of initial conditions. Thus, we consider two sets of initial conditions: an initial displacement and an initial momentum excitation of a single bead. After establishing the regime of sufficiently strong disorder, we focus our study on the role of nonlinearity for both sets of initial conditions. By increasing the initial excitation amplitudes we are able to identify three distinct dynamical regimes with different energy transport properties: a near linear, a weakly nonlinear, and a highly nonlinear regime. Although energy spreading is found to be increasing for higher nonlinearities, in the weakly nonlinear regime no clear asymptotic behavior of the spreading is found. In this regime, we additionally find that energy, initially trapped in a localized region, can be eventually detrapped and this has a direct influence on the fluctuations of the energy spreading. We also demonstrate that in the highly nonlinear regime, the differences in energy transport between the two sets of initial conditions vanish. Actually, in this regime the energy is almost ballistically transported through shocklike excitations.

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We investigate dynamically and statistically diffusive motion in a Klein-Gordon particle chain in the presence of disorder. In particular, we examine a low energy (subdiffusive) and a higher energy (self-trapping) case and verify that subdiffusive spreading is always observed. We then carry out a statistical analysis of the motion, in both cases, in the sense of the Central Limit Theorem and present evidence of different chaos behaviors, for various groups of particles. Integrating the equations of motion for times as long as 10(9), our probability distribution functions always tend to Gaussians and show that the dynamics does not relax onto a quasi-periodic Kolmogorov-Arnold-Moser torus and that diffusion continues to spread chaotically for arbitrarily long times.

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Do nonlinear waves destroy Anderson localization? Computational and experimental studies yield subdiffusive nonequilibrium wave packet spreading. Chaotic dynamics and phase decoherence assumptions are used for explaining the data. We perform a quantitative analysis of the nonequilibrium chaos assumption and compute the time dependence of main chaos indicators--Lyapunov exponents and deviation vector distributions. We find a slowing down of chaotic dynamics, which does not cross over into regular dynamics up to the largest observed time scales, still being fast enough to allow for a thermalization of the spreading wave packet. Strongly localized chaotic spots meander through the system as time evolves. Our findings confirm for the first time that nonequilibrium chaos and phase decoherence persist, fueling the prediction of a complete delocalization.

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We probe the limits of nonlinear wave spreading in disordered chains which are known to localize linear waves. We particularly extend recent studies on the regimes of strong and weak chaos during subdiffusive spreading of wave packets [Europhys. Lett. 91, 30001 (2010)] and consider strong disorder, which favors Anderson localization. We probe the limit of infinite disorder strength and study Fröhlich-Spencer-Wayne models. We find that the assumption of chaotic wave packet dynamics and its impact on spreading is in accord with all studied cases. Spreading appears to be asymptotic, without any observable slowing down. We also consider chains with spatially inhomogeneous nonlinearity, which give further support to our findings and conclusions.

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A numerical and analytical study of the relaxation to equilibrium of both the Fermi-Pasta-Ulam (FPU) α-model and the integrable Toda model, when the fundamental mode is initially excited, is reported. We show that the dynamics of both systems is almost identical on the short term, when the energies of the initially unexcited modes grow in geometric progression with time, through a secular avalanche process. At the end of this first stage of the dynamics, the time-averaged modal energy spectrum of the Toda system stabilizes to its final profile, well described, at low energy, by the spectrum of a q-breather. The Toda equilibrium state is clearly shown to describe well the long-living quasi-state of the FPU system. On the long term, the modal energy spectrum of the FPU system slowly detaches from the Toda one by a diffusive-like rising of the tail modes, and eventually reaches the equilibrium flat shape. We find a simple law describing the growth of tail modes, which enables us to estimate the time-scale to equipartition of the FPU system, even when, at small energies, it becomes unobservable.

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We study the spreading of single-site excitations in one-dimensional disordered Klein-Gordon chains with tunable nonlinearity |u(l)|(σ)u(l) for different values of σ. We perform extensive numerical simulations where wave packets are evolved (a) without and (b) with dephasing in normal-mode space. Subdiffusive spreading is observed with the second moment of wave packets growing as t(α). The dependence of the numerically computed exponent α on σ is in very good agreement with our theoretical predictions both for the evolution of the wave packet with and without dephasing (for σ≥2 in the latter case). We discuss evidence of the existence of a regime of strong chaos and observe destruction of Anderson localization in the packet tails for small values of σ.

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We present and compare different numerical schemes for the integration of the variational equations of autonomous Hamiltonian systems whose kinetic energy is quadratic in the generalized momenta and whose potential is a function of the generalized positions. We apply these techniques to Hamiltonian systems of various degrees of freedom and investigate their efficiency in accurately reproducing well-known properties of chaos indicators such as the Lyapunov characteristic exponents and the generalized alignment indices. We find that the best numerical performance is exhibited by the "tangent map method," a scheme based on symplectic integration techniques which proves to be optimal in speed and accuracy. According to this method, a symplectic integrator is used to approximate the solution of the Hamilton equations of motion by the repeated action of a symplectic map S , while the corresponding tangent map TS is used for the integration of the variational equations. A simple and systematic technique to construct TS is also presented.

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We consider the spatiotemporal evolution of a wave packet in disordered nonlinear Schrödinger and anharmonic oscillator chains. In the absence of nonlinearity all eigenstates are spatially localized with an upper bound on the localization length (Anderson localization). Nonlinear terms in the equations of motion destroy the Anderson localization due to nonintegrability and deterministic chaos. At least a finite part of an initially localized wave packet will subdiffusively spread without limits. We analyze the details of this spreading process. We compare the evolution of single-site, single-mode, and general finite-size excitations and study the statistics of detrapping times. We investigate the properties of mode-mode resonances, which are responsible for the incoherent delocalization process.

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In the absence of nonlinearity all eigenmodes of a chain with disorder are spatially localized (Anderson localization). The width of the eigenvalue spectrum and the average eigenvalue spacing inside the localization volume set two frequency scales. An initially localized wave packet spreads in the presence of nonlinearity. Nonlinearity introduces frequency shifts, which define three different evolution outcomes: (i) localization as a transient, with subsequent subdiffusion; (ii) the absence of the transient and immediate subdiffusion; (iii) self-trapping of a part of the packet and subdiffusion of the remainder. The subdiffusive spreading is due to a finite number of packet modes being resonant. This number does not change on average and depends only on the disorder strength. Spreading is due to corresponding weak chaos inside the packet, which slowly heats the cold exterior. The second moment of the packet grows as t;{alpha}. We find alpha=1/3.