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We study quasiperiodicity-induced localization of waves in strongly precompressed granular chains. We propose three different set-ups, inspired by the Aubry-André (AA) model, of quasiperiodic chains; and we use these models to compare the effects of on-site and off-site quasiperiodicity in nonlinear lattices. When there is purely on-site quasiperiodicity, which we implement in two different ways, we show for a chain of spherical particles that there is a localization transition (as in the original AA model). However, we observe no localization transition in a chain of cylindrical particles in which we incorporate quasiperiodicity in the distribution of contact angles between adjacent cylinders by making the angle periodicity incommensurate with that of the chain. For each of our three models, we compute the Hofstadter spectrum and the associated Minkowski-Bouligand fractal dimension, and we demonstrate that the fractal dimension decreases as one approaches the localization transition (when it exists). We also show, using the chain of cylinders as an example, how to recover the Hofstadter spectrum from the system dynamics. Finally, in a suite of numerical computations, we demonstrate localization and also that there exist regimes of ballistic, superdiffusive, diffusive and subdiffusive transport. Our models provide a flexible set of systems to study quasiperiodicity-induced analogues of Anderson phenomena in granular chains that one can tune controllably from weakly to strongly nonlinear regimes.This article is part of the theme issue 'Nonlinear energy transfer in dynamical and acoustical systems'.

The original version of this Article contained an error in second sentence of the Acknowledgements, which incorrectly read 'J.Y. and P.G.K. also acknowledge support from US-ARO (W911NF-15-1-0604) and US-AFOSR (FA9550-17-1-011), and P.G.K. also gratefully acknowledges support from the Stavros Niarchos Foundation via the Greek Diaspora Fellowship Program.' The correct version states 'US-AFOSR (FA9550-17-1-0114)' in place of 'US-AFOSR (FA9550-17-1-011)'. This has been corrected in both the PDF and HTML versions of the Article.

Energy transport properties in heterogeneous materials have attracted scientific interest for more than half of a century, and they continue to offer fundamental and rich questions. One of the outstanding challenges is to extend Anderson theory for uncorrelated and fully disordered lattices in condensed-matter systems to physical settings in which additional effects compete with disorder. Here we present the first systematic experimental study of energy transport and localization properties in simultaneously disordered and nonlinear granular crystals. In line with prior theoretical studies, we observe in our experiments that disorder and nonlinearity-which individually favor energy localization-can effectively cancel each other out, resulting in the destruction of wave localization. We also show that the combined effect of disorder and nonlinearity can enable manipulation of energy transport speed in granular crystals. Specifically, we experimentally demonstrate superdiffusive transport. Furthermore, our numerical computations suggest that subdiffusive transport should be attainable by controlling the strength of the system's external precompression force.

The existence of breather-type solutions, i.e., solutions that are periodic in time and exponentially localized in space, is a very unusual feature for continuum, nonlinear wave-type equations. Following an earlier work establishing a theorem for the existence of such structures, we bring to bear a combination of analysis-inspired numerical tools that permit the construction of such waveforms to a desired numerical accuracy. In addition, this enables us to explore their numerical stability. Our computations show that for the spatially heterogeneous form of the ϕ4 model considered herein, the breather solutions are generically unstable. Their instability seems to generically favor the motion of the relevant structures. We expect that these results may inspire further studies towards the identification of stable continuous breathers in spatially heterogeneous, continuum nonlinear wave equation models.

Motivated by an exact mapping between equilibrium properties of a one-dimensional chain of quantum Ising spins in a transverse field (the transverse field Ising (TFI) model) and a two-dimensional classical array of particles in double-well potentials (the "ϕ4 model") with weak inter-chain coupling, we explore connections between the driven variants of the two systems. We argue that coupling between the fundamental topological solitary waves in the form of kinks between neighboring chains in the classical ϕ4 system is the analog of the competing effect of the transverse field on spin flips in the quantum TFI model. As an example application, we mimic simplified measurement protocols in a closed quantum model system by studying the classical ϕ4 model subjected to periodic perturbations. This reveals memory/loss of memory and coherence/decoherence regimes, whose quantum analogs are essential in annealing phenomena. In particular, we examine regimes where the topological excitations control the thermal equilibration following perturbations. This paves the way for further explorations of the analogy between lower-dimensional linear quantum and higher-dimensional classical nonlinear systems., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In the present work we explore the interaction of a quasi-one-dimensional line kink of the sine-Gordon equation moving in two-dimensional spatial domains. We develop an effective equation describing the kink motion, characterizing its center position dynamics as a function of the transverse variable. The relevant description is valid both in the Hamiltonian realm and in the nonconservative one bearing gain and loss. We subsequently examine a variety of different scenarios, without and with a spatially dependent heterogeneity. The latter is considered both to be one dimensional (y independent) and genuinely two dimensional. The spectral features and the dynamical interaction of the kink with the heterogeneity are considered and comparison with the effective quasi-one-dimensional description (characterizing the kink center as a function of the transverse variable) is also provided. Generally, good agreement is found between the analytical predictions and the computational findings in the different cases considered.

We experimentally realize the Peregrine soliton in a highly particle-imbalanced two-component repulsive Bose-Einstein condensate in the immiscible regime. The effective focusing dynamics and resulting modulational instability of the minority component provide the opportunity to dynamically create a Peregrine soliton with the aid of an attractive potential well that seeds the initial dynamics. The Peregrine soliton formation is highly reproducible, and our experiments allow us to separately monitor the minority and majority components, and to compare with the single component dynamics in the absence or presence of the well with varying depths. We showcase the centrality of each of the ingredients leveraged herein. Numerical corroborations and a theoretical basis for our findings are provided through three-dimensional simulations emulating the experimental setting and via a one-dimensional analysis further exploring its evolution dynamics.

We explore the inclusion of vaccination in compartmental epidemiological models concerning the delta and omicron variants of the SARS-CoV-2 virus that caused the COVID-19 pandemic. We expand on our earlier compartmental-model work by incorporating vaccinated populations. We present two classes of models that differ depending on the immunological properties of the variant. The first one is for the delta variant, where we do not follow the dynamics of the vaccinated individuals since infections of vaccinated individuals were rare. The second one for the far more contagious omicron variant incorporates the evolution of the infections within the vaccinated cohort. We explore comparisons with available data involving two possible classes of counts, fatalities and hospitalizations. We present our results for two regions, Andalusia and Switzerland (including the Principality of Liechtenstein), where the necessary data are available. In the majority of the considered cases, the models are found to yield good agreement with the data and have a reasonable predictive capability beyond their training window, rendering them potentially useful tools for the interpretation of the COVID-19 and further pandemic waves, and for the design of intervention strategies during these waves., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

We consider a dimer lattice of the Fermi-Pasta-Ulam-Tsingou (FPUT) type, where alternating linear couplings have a controllably small difference and the cubic nonlinearity (β-FPUT) is the same for all interaction pairs. We use a weakly nonlinear formal reduction within the lattice band gap to obtain a continuum, nonlinear Dirac-type system. We derive the Dirac soliton profiles and the model's conservation laws analytically. We then examine the cases of the semi-infinite and the finite domains and illustrate how the soliton solutions of the bulk problem can be glued to the boundaries for different types of boundary conditions. We thus explain the existence of various kinds of nonlinear edge states in the system, of which only one leads to the standard topological edge states observed in the linear limit. We finally examine the stability of bulk and edge states and verify them through direct numerical simulations, in which we observe a solitonlike wave setting into motion due to the instability.

Deflation is an efficient numerical technique for identifying new branches of steady state solutions to nonlinear partial differential equations. Here, we demonstrate how to extend deflation to discover new periodic orbits in nonlinear dynamical lattices. We employ our extension to identify discrete breathers, which are generic exponentially localized, time-periodic solutions of such lattices. We compare different approaches to using deflation for periodic orbits, including ones based on Fourier decomposition of the solution, as well as ones based on the solution's energy density profile. We demonstrate the ability of the method to obtain a wide variety of multibreather solutions without prior knowledge about their spatial profile., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

In the present study the interaction of a sine-Gordon kink with a localized inhomogeneity is considered. In the absence of dissipation, the inhomogeneity considered is found to impose a potential energy barrier. The motion of the kink for near-critical values of velocities separating transmission from barrier reflection is studied. Moreover, the existence and stability properties of the kink at the relevant saddle point are examined and its dynamics is found to be accurately captured by effective low-dimensional models. In the case where there is dissipation in the system, below the threshold value of the current, a stable kink is found to exist in the immediate vicinity of the barrier. The effective particle motion of the kink is investigated obtaining very good agreement with the result of the original field model. Both one and two degree-of-freedom settings are examined with the latter being more efficient than the former in capturing the details of the kink motion.

In the present work we study coherent structures in a one-dimensional discrete nonlinear Schrödinger lattice in which the coupling between waveguides is periodically modulated. Numerical experiments with single-site initial conditions show that, depending on the power, the system exhibits two fundamentally different behaviors. At low power, initial conditions with intensity concentrated in a single site give rise to transport, with the energy moving unidirectionally along the lattice, whereas high-power initial conditions yield stationary solutions. We explain these two behaviors, as well as the nature of the transition between the two regimes, by analyzing a simpler model where the couplings between waveguides are given by step functions. For the original model, we numerically construct both stationary and moving coherent structures, which are solutions reproducing themselves exactly after an integer multiple of the coupling period. For the stationary solutions, which are true periodic orbits, we use Floquet analysis to determine the parameter regime for which they are spectrally stable. Typically, the traveling solutions are characterized by having small-amplitude oscillatory tails, although we identify a set of parameters for which these tails disappear. These parameters turn out to be independent of the lattice size, and our simulations suggest that for these parameters, numerically exact traveling solutions are stable.

We introduce a methodology for seeking conservation laws within a Hamiltonian dynamical system, which we term "neural deflation." Inspired by deflation methods for steady states of dynamical systems, we propose to iteratively train a number of neural networks to minimize a regularized loss function accounting for the necessity of conserved quantities to be in involution and enforcing functional independence thereof consistently in the infinite-sample limit. The method is applied to a series of integrable and nonintegrable lattice differential-difference equations. In the former, the predicted number of conservation laws extensively grows with the number of degrees of freedom, while for the latter, it generically stops at a threshold related to the number of conserved quantities in the system. This data-driven tool could prove valuable in assessing a model's conserved quantities and its potential integrability.

Metapopulation models have been a popular tool for the study of epidemic spread over a network of highly populated nodes (cities, provinces, countries) and have been extensively used in the context of the ongoing COVID-19 pandemic. In the present work, we revisit such a model, bearing a particular case example in mind, namely that of the region of Andalusia in Spain during the period of the summer-fall of 2020 (i.e., between the first and second pandemic waves). Our aim is to consider the possibility of incorporation of mobility across the province nodes focusing on mobile-phone time-dependent data, but also discussing the comparison for our case example with a gravity model, as well as with the dynamics in the absence of mobility. Our main finding is that mobility is key toward a quantitative understanding of the emergence of the second wave of the pandemic and that the most accurate way to capture it involves dynamic (rather than static) inclusion of time-dependent mobility matrices based on cell-phone data. Alternatives bearing no mobility are unable to capture the trends revealed by the data in the context of the metapopulation model considered herein., (© 2023. The Author(s), under exclusive licence to Society for Mathematical Biology.)

This work focuses on the study of time-periodic solutions, including breathers, in a nonlinear lattice consisting of elements whose contacts alternate between strain hardening and strain softening. The existence, stability, and bifurcation structure of such solutions, as well as the system dynamics in the presence of damping and driving, are studied systematically. It is found that the linear resonant peaks in the system bend toward the frequency gap in the presence of nonlinearity. The time-periodic solutions that lie within the frequency gap compare well to Hamiltonian breathers if the damping and driving are small. In the Hamiltonian limit of the problem, we use a multiple scale analysis to derive a nonlinear Schrödinger equation to construct both acoustic and optical breathers. The latter compare very well with the numerically obtained breathers in the Hamiltonian limit.

We consider the instability and stability of periodic stationary solutions to the classical ϕ^{4} equation numerically. In the superluminal regime, the model possesses dnoidal and cnoidal waves. The former are modulationally unstable and the spectrum forms a figure eight intersecting at the origin of the spectral plane. The latter can be modulationally stable, and the spectrum near the origin in that case is represented by vertical bands along the purely imaginary axis. The instability of the cnoidal states in that case stems from elliptical bands of complex eigenvalues far from the spectral plane origin. In the subluminal regime, there exist only snoidal waves which are modulationally unstable. Considering the subharmonic perturbations, we show that the snoidal waves in the subluminal regime are spectrally unstable with respect to all subharmonic perturbations, while for the dnoidal and cnoidal waves in the superluminal regime, the transition between the spectrally stable state and the spectrally unstable state occurs through a Hamiltonian Hopf bifurcation. The dynamical evolution of the unstable states is also considered, leading to some interesting localization events on the spatio-temporal backgrounds.

In the present work we explore the concept of solitary wave billiards. That is, instead of a point particle, we examine a solitary wave in an enclosed region and examine its collision with the boundaries and the resulting trajectories in cases which for particle billiards are known to be integrable and for cases that are known to be chaotic. A principal conclusion is that solitary wave billiards are generically found to be chaotic even in cases where the classical particle billiards are integrable. However, the degree of resulting chaoticity depends on the particle speed and on the properties of the potential. Furthermore, the nature of the scattering of the deformable solitary wave particle is elucidated on the basis of a negative Goos-Hänchen effect which, in addition to a trajectory shift, also results in an effective shrinkage of the billiard domain.

In the present work we revisit the Salerno model as a prototypical system that interpolates between a well-known integrable system (the Ablowitz-Ladik lattice) and an experimentally tractable, nonintegrable one (the discrete nonlinear Schrödinger model). The question we ask is, for "generic" initial data, how close are the integrable to the nonintegrable models? Our more precise formulation of this question is, How well is the constancy of formerly conserved quantities preserved in the nonintegrable case? Upon examining this, we find that even slight deviations from integrability can be sensitively felt by measuring these formerly conserved quantities in the case of the Salerno model. However, given that the knowledge of these quantities requires a deep physical and mathematical analysis of the system, we seek a more "generic" diagnostic towards a manifestation of integrability breaking. We argue, based on our Salerno model computations, that the full spectrum of Lyapunov exponents could be a sensitive diagnostic to that effect.

We present a mathematical model that describes how tumour heterogeneity evolves in a tissue slice that is oxygenated by a single blood vessel. Phenotype is identified with the stemness level of a cell and determines its proliferative capacity, apoptosis propensity and response to treatment. Our study is based on numerical bifurcation analysis and dynamical simulations of a system of coupled, non-local (in phenotypic "space") partial differential equations that link the phenotypic evolution of the tumour cells to local tissue oxygen levels. In our formulation, we consider a 1D geometry where oxygen is supplied by a blood vessel located on the domain boundary and consumed by the tumour cells as it diffuses through the tissue. For biologically relevant parameter values, the system exhibits multiple steady states; in particular, depending on the initial conditions, the tumour is either eliminated ("tumour-extinction") or it persists ("tumour-invasion"). We conclude by using the model to investigate tumour responses to radiotherapy, and focus on identifying radiotherapy strategies which can eliminate the tumour. Numerical simulations reveal how phenotypic heterogeneity evolves during treatment and highlight the critical role of tissue oxygen levels on the efficacy of radiation protocols that are commonly used in the clinic., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

We consider a previously experimentally realized discrete model that describes a mechanical metamaterial consisting of a chain of pairs of rigid units connected by flexible hinges. Upon analyzing the linear band structure of the model, we identify parameter regimes in which this system may possess discrete breather solutions with frequencies inside the gap between optical and acoustic dispersion bands. We compute numerically exact solutions of this type for several different parameter regimes and investigate their properties and stability. Our findings demonstrate that upon appropriate parameter tuning within experimentally tractable ranges, the system exhibits a plethora of discrete breathers, with multiple branches of solutions that feature period-doubling and symmetry-breaking bifurcations, in addition to other mechanisms of stability change such as saddle-center and Hamiltonian Hopf bifurcations. The relevant stability analysis is corroborated by direct numerical computations examining the dynamical properties of the system and paving the way for potential further experimental exploration of this rich nonlinear dynamical lattice setting.

It is widely accepted that the number of reported cases during the first stages of the COVID-19 pandemic severely underestimates the number of actual cases. We leverage delay embedding theorems of Whitney and Takens and use Gaussian process regression to estimate the number of cases during the first 2020 wave based on the second wave of the epidemic in several European countries, South Korea and Brazil. We assume that the second wave was more accurately monitored, even though we acknowledge that behavioural changes occurred during the pandemic and region- (or country-) specific monitoring protocols evolved. We then construct a manifold diffeomorphic to that of the implied original dynamical system, using fatalities or hospitalizations only. Finally, we restrict the diffeomorphism to the reported cases coordinate of the dynamical system. Our main finding is that in the European countries studied, the actual cases are under-reported by as much as 50%. On the other hand, in South Korea-which had a proactive mitigation approach-a far smaller discrepancy between the actual and reported cases is predicted, with an approximately 18% predicted underestimation. We believe that our backcasting framework is applicable to other epidemic outbreaks where (due to limited or poor quality data) there is uncertainty around the actual cases., (© 2022 The Authors.)

Here we revisit the topic of stationary and propagating solitonic excitations in self-repulsive three-dimensional (3D) Bose-Einstein condensates by quantitatively comparing theoretical analysis and associated numerical computations with our experimental results. Motivated by numerous experimental efforts, including our own herein, we use fully 3D numerical simulations to explore the existence, stability, and evolution dynamics of planar dark solitons. This also allows us to examine their instability-induced decay products including solitonic vortices and vortex rings. In the trapped case and with no adjustable parameters, our numerical findings are in correspondence with experimentally observed coherent structures. Without a longitudinal trap, we identify numerically exact traveling solutions and quantify how their transverse destabilization threshold changes as a function of the solitary wave speed., (Creative Commons Attribution license.)

Many approaches using compartmental models have been used to study the COVID-19 pandemic, with machine learning methods applied to these models having particularly notable success. We consider the Susceptible-Infected-Confirmed-Recovered-Deceased (SICRD) compartmental model, with the goal of estimating the unknown infected compartment I , and several unknown parameters. We apply a variation of a "Physics Informed Neural Network" (PINN), which uses knowledge of the system to aid learning. First, we ensure estimation is possible by verifying the model's identifiability. Then, we propose a wavelet transform to process data for the network training. Finally, our central result is a novel modification of the PINN's loss function to reduce the number of simultaneously considered unknowns. We find that our modified network is capable of stable, efficient, and accurate estimation, while the unmodified network consistently yields incorrect values. The modified network is also shown to be efficient enough to be applied to a model with time-varying parameters. We present an application of our model results for ranking states by their estimated relative testing efficiency. Our findings suggest the effectiveness of our modified PINN network, especially in the case of multiple unknown variables.