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## Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines

Fonte: National Academy of Sciences
Publicador: National Academy of Sciences

Tipo: Artigo de Revista Científica

Português

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Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well defined internal mechanical motions to various initial deformations and that these motions are robust against external perturbations. We show that this behavior is not characteristic for random elastic networks. However, special network architectures with such properties can be designed by evolutionary optimization methods. Using them, an example of an artificial elastic network, operating as a cyclic machine powered by ligand binding, is constructed.

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## Fluctuations of fish populations and the magnifying effects of fishing

Fonte: National Academy of Sciences
Publicador: National Academy of Sciences

Tipo: Artigo de Revista Científica

Português

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A central and classic question in ecology is what causes populations to fluctuate in abundance. Understanding the interaction between natural drivers of fluctuating populations and human exploitation is an issue of paramount importance for conservation and natural resource management. Three main hypotheses have been proposed to explain fluctuations: (i) species interactions, such as predator–prey interactions, cause fluctuations, (ii) strongly nonlinear single-species dynamics cause fluctuations, and (iii) environmental variation cause fluctuations. We combine a general fisheries model with data from a global sample of fish species to assess how two of these hypothesis, nonlinear single-species dynamics and environmental variation, interact with human exploitation to affect the variability of fish populations. In contrast with recent analyses that suggest fishing drives increased fluctuations by changing intrinsic nonlinear dynamics, we show that single-species nonlinear dynamics alone, both in the presence and absence of fisheries, are unlikely to drive deterministic fluctuations in fish; nearly all fish populations fall into regions of stable dynamics. However, adding environmental variation dramatically alters the consequences of exploitation on the temporal variability of populations. In a variable environment...

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## Estimation of Instantaneous Complex Dynamics through Lyapunov Exponents: A Study on Heartbeat Dynamics

Fonte: Public Library of Science
Publicador: Public Library of Science

Tipo: Artigo de Revista Científica

Português

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#Biology and Life Sciences#Biotechnology#Bioengineering#Biomedical Engineering#Computer and Information Sciences#Systems Science#Nonlinear Dynamics#Physical Sciences#Mathematics#Probability Theory#Stochastic Processes

Measures of nonlinearity and complexity, and in particular the study of Lyapunov exponents, have been increasingly used to characterize dynamical properties of a wide range of biological nonlinear systems, including cardiovascular control. In this work, we present a novel methodology able to effectively estimate the Lyapunov spectrum of a series of stochastic events in an instantaneous fashion. The paradigm relies on a novel point-process high-order nonlinear model of the event series dynamics. The long-term information is taken into account by expanding the linear, quadratic, and cubic Wiener-Volterra kernels with the orthonormal Laguerre basis functions. Applications to synthetic data such as the Hénon map and Rössler attractor, as well as two experimental heartbeat interval datasets (i.e., healthy subjects undergoing postural changes and patients with severe cardiac heart failure), focus on estimation and tracking of the Instantaneous Dominant Lyapunov Exponent (IDLE). The novel cardiovascular assessment demonstrates that our method is able to effectively and instantaneously track the nonlinear autonomic control dynamics, allowing for complexity variability estimations.

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## The Madden-Julian oscillation and nonlinear moisture modes; MJO and nonlinear moisture modes

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 245 p.

Português

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The Madden-Julian oscillation (MJO), the dominant tropical intraseasonal variability with widespread meteorological impacts, continues to puzzle the climate research community on both theoretical and modeling fronts. Motivated by a recent interest in the role of humidity in tropical dynamics, this thesis hypothesizes that the MJO is a nonlinear moisture mode whose existence depends on moisture-convection feedback (the feedback between deep convection and environmental free-tropospheric humidity), and that weak moisture convection feedback in general circulation models accounts for their deficiencies with the MJO simulations. Moisture modes are found to exist in a large class of linear primitive equation models on the equatorial beta-plane. For models with standard quasi-equilibrium parameterizations,perturbation expansion analyses demonstrate that the weak temperature gradient (WTG) approximation of Sobel et al. describes the small-scale limit of the moisture mode accurately,with the small expansion parameter being the ratio between temperature tendency and adiabatic cooling. Under the WTG balance, the only leading order variables are humidity and vertical motion. Analyses of three models in the literature show that a moisture mode is unstable if moist static energy (MSE) sources such as cloud radiative forcing or gust-enhanced surface heat flux exceed the MSE export. Numerical calculations of a single-column model under the WTG configuration show that a realistic convective scheme can reproduce moisture mode instability. Sensitivity tests on the strength of moisture-convection feedback in the Emanuel scheme indicate that such a feedback is essential for moisture mode instability...

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## Nonlinear dynamics of two-color optical vortices in lithium niobate crystals

Fonte: Universidade Nacional da Austrália
Publicador: Universidade Nacional da Austrália

Tipo: Journal article; Published Version
Formato: 15 pages

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#Nonlinear optics, transverse effects in#Nonlinear optics#Frequency conversion#Self-action effects#Photorefractive nonlinear optics

We study experimentally the nonlinear dynamics of two-color
optical vortex beams in the presence of second-harmonic generation combined
with the effects of photo- and thermal refraction, as well as self- and
induced-phase modulation.We use an iron-doped lithium niobate crystal as
a nonlinear medium for the vortex propagation and observe experimentally,
depending on the laser wavelength, a decay of a double-charge vortex, splitting
and reshaping of background beam, pattern formation, and controllable
nonlinear rotation of a vortex pair.; Affiliation in article: Dreischuh, Alexander and Saltiel, Solomon, also with Sofia University, Faculty of Physics, Bulgaria.

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## Nonlinear Gamow vectors, shock waves and irreversibility in optically nonlocal media

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 04/08/2015
Português

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Dispersive shock waves dominate wave-breaking phenomena in Hamiltonian
systems. In the absence of loss, these highly irregular and disordered waves
are potentially reversible. However, no experimental evidence has been given
about the possibility of inverting the dynamics of a dispersive shock wave and
turn it into a regular wave-front. Nevertheless, the opposite scenario, i.e., a
smooth wave generating turbulent dynamics is well studied and observed in
experiments. Here we introduce a new theoretical formulation for the dynamics
in a highly nonlocal and defocusing medium described by the nonlinear
Schroedinger equation. Our theory unveils a mechanism that enhances the degree
of irreversibility. This mechanism explains why a dispersive shock cannot be
reversed in evolution even for an arbitrarirly small amount of loss. Our theory
is based on the concept of nonlinear Gamow vectors, i.e., power dependent
generalizations of the counter-intuitive and hereto elusive exponentially
decaying states in Hamiltonian systems. We theoretically show that nonlinear
Gamow vectors play a fundamental role in nonlinear Schroedinger models: they
may be used as a generalized basis for describing the dynamics of the shock
waves, and affect the degree of irreversibility of wave-breaking phenomena.
Gamow vectors allow to analytically calculate the amount of breaking of
time-reversal with a quantitative agreement with numerical solutions. We also
show that a nonlocal nonlinear optical medium may act as a simulator for the
experimental investigation of quantum irreversible models...

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## Quasiclassical Calculations of Wigner Functions in Nonlinear Beam Dynamics

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 02/06/2001
Português

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#Physics - Accelerator Physics#Mathematical Physics#Nonlinear Sciences - Pattern Formation and Solitons#Physics - Computational Physics#Quantum Physics

We present the application of variational-wavelet analysis to
numerical/analytical calculations of Wigner functions in (nonlinear)
quasiclassical beam dynamics problems. (Naive) deformation quantization and
multiresolution representations are the key points. We construct the
representation via multiscale expansions in generalized coherent states or
high-localized nonlinear eigenmodes in the base of compactly supported wavelets
and wavelet packets.; Comment: 3 pages, 2 figures, JAC2001.cls, submitted to Proc. Particle
Accelerator Conference (PAC2001), Chicago, June 18-22, 2001

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## Fluid Models for Kinetic Effects on Coherent Nonlinear Alfven Waves. I. Fundamental Theory

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 30/12/1996
Português

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#Physics - Plasma Physics#Astrophysics#Nonlinear Sciences - Adaptation and Self-Organizing Systems#Physics - Space Physics

Collisionless regime kinetic models for coherent nonlinear Alfven wave
dynamics are studied using fluid moment equations with an approximate closure
anzatz. Resonant particle effects are modelled by incorporating an additional
term representing dissipation akin to parallel heat conduction. Unlike
collisional dissipation, parallel heat conduction is presented by an integral
operator. The modified derivative nonlinear Schrodinger equation thus has a
spatially nonlocal nonlinear term describing the long-time evolution of the
envelope of parallel-propagating Alfven waves, as well. Coefficients in the
nonlinear terms are free of the 1/(1-beta) singularity usually encountered in
previous analyses, and have very a simple form which clarifies the physical
processes governing the large amplitude Alfvenic nonlinear dynamics. The
nonlinearity appears via coupling of an Alfvenic mode to a kinetic ion-acoustic
mode. Damping of the nonlinear Alfven wave appears via strong Landau damping of
the ion-acoustic wave when the electron-to-ion temperature ratio is close to
unity. For a (slightly) obliquely propagating wave, there are finite Larmor
radius corrections in the dynamical equation. This effect depends on the angle
of wave propagation relative to B_0 and vanishes for the limit of strictly
parallel propagation. Explicit magnetic perturbation envelope equations
amenable to further analysis and numerical solution are obtained. Implications
of these models for collisionless shock dynamics are discussed.; Comment: 34 pages (including 6 figures)

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## Fluid Models for Kinetic Effects on Coherent Nonlinear Alfven Waves. II. Numerical Solutions

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 30/12/1996
Português

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587.46023%

#Physics - Plasma Physics#Astrophysics#Nonlinear Sciences - Adaptation and Self-Organizing Systems#Nonlinear Sciences - Pattern Formation and Solitons#Physics - Space Physics

The influence of various kinetic effects (e.g. Landau damping, diffusive and
collisional dissipation, and finite Larmor radius terms) on the nonlinear
evolution of finite amplitude Alfvenic wave trains in a finite-beta environment
is systematically investigated using a novel, kinetic nonlinear Schrodinger
(KNLS) equation. The dynamics of Alfven waves is sensitive to the sense of
polarization as well as the angle of propagation with respect to the ambient
magnetic field. Numerical solution for the case with Landau damping reveals the
formation of dissipative structures, which are quasi-stationary, S-polarized
directional (and rotational) discontinuities which self-organize from parallel
propagating, linearly polarized waves. Parallel propagating circularly
polarized packets evolve to a few circularly polarized Alfven harmonics on
large scales. Stationary arc-polarized rotational discontinuities form from
obliquely propagating waves. Collisional dissipation, even if weak, introduces
enhanced wave damping when beta is very close to unity. Cyclotron motion
effects on resonant particle interactions introduce cyclotron resonance into
the nonlinear Alfven wave dynamics.; Comment: 38 pages (including 23 figures and 1 table)

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## Dissipative Dynamics of Collisionless Nonlinear Alfven Wave Trains

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 25/07/1997
Português

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#Physics - Space Physics#Astrophysics#Nonlinear Sciences - Adaptation and Self-Organizing Systems#Nonlinear Sciences - Pattern Formation and Solitons#Physics - Plasma Physics

The nonlinear dynamics of collisionless Alfven trains, including resonant
particle effects is studied using the kinetic nonlinear Schroedinger (KNLS)
equation model. Numerical solutions of the KNLS reveal the dynamics of Alfven
waves to be sensitive to the sense of polarization as well as the angle of
propagation with respect to the ambient magnetic field. The combined effects of
both wave nonlinearity and Landau damping result in the evolutionary formation
of stationaryOA S- and arc-polarized directional and rotational
discontinuities. These waveforms are freqently observed in the interplanetary
plasma.; Comment: REVTeX, 6 pages (including 5 figures). This and other papers may be
found at http://sdphpd.ucsd.edu/~medvedev/papers.html

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## A framework for the local information dynamics of distributed computation in complex systems

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Português

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488.6818%

#Nonlinear Sciences - Cellular Automata and Lattice Gases#Computer Science - Information Theory#Nonlinear Sciences - Adaptation and Self-Organizing Systems#Nonlinear Sciences - Pattern Formation and Solitons#Physics - Data Analysis, Statistics and Probability#94A15

The nature of distributed computation has often been described in terms of
the component operations of universal computation: information storage,
transfer and modification. We review the first complete framework that
quantifies each of these individual information dynamics on a local scale
within a system, and describes the manner in which they interact to create
non-trivial computation where "the whole is greater than the sum of the parts".
We describe the application of the framework to cellular automata, a simple yet
powerful model of distributed computation. This is an important application,
because the framework is the first to provide quantitative evidence for several
important conjectures about distributed computation in cellular automata: that
blinkers embody information storage, particles are information transfer agents,
and particle collisions are information modification events. The framework is
also shown to contrast the computations conducted by several well-known
cellular automata, highlighting the importance of information coherence in
complex computation. The results reviewed here provide important quantitative
insights into the fundamental nature of distributed computation and the
dynamics of complex systems, as well as impetus for the framework to be applied
to the analysis and design of other systems.; Comment: 44 pages...

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## Local Analysis of Nonlinear RMS Envelope Dynamics

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 13/08/2000
Português

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#Physics - Accelerator Physics#Mathematical Physics#Nonlinear Sciences - Adaptation and Self-Organizing Systems#Physics - Computational Physics

We present applications of variational -- wavelet approach to nonlinear
(rational) rms envelope dynamics. We have the solution as a multiresolution
(multiscales) expansion in the base of compactly supported wavelet basis.; Comment: 3 pages, 4 figures, JAC2000.cls, Proc. European Particle Accelerator
Conf., EPAC00, Vienna, 2000

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## Dynamics of Immobilized Flagella

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Português

Relevância na Pesquisa

489.9728%

#Physics - Biological Physics#Nonlinear Sciences - Adaptation and Self-Organizing Systems#Nonlinear Sciences - Pattern Formation and Solitons#Physics - Chemical Physics#Physics - Fluid Dynamics#Quantitative Biology - Cell Behavior#Quantitative Biology - Quantitative Methods#Quantitative Biology - Subcellular Processes

Although the auger-like 'swimming' motility of the African trypanosome was
described upon its discovery over one hundred years ago, the precise
biomechanical and biophysical properties of trypanosome flagellar motion has
not been elucidated. In this study, we describe five different modes of
flagellar beat/wave patterns in African trypanosomes by microscopically
examining the flagellar movements of chemically tethered cells. The dynamic
nature of the different beat/wave patterns suggests that flagellar motion in
Trypanosoma brucei is a complex mixture of oscillating waves, rigid bends,
helical twists and non-linear waves. Interestingly, we have observed
soliton-like depression waves along the flagellar membrane, suggesting a
nonlinear mechanism for the dynamics of this system. The physical model is
inspired by the 2-dimensional elastic dynamics of a beam, and by taking into
account uniform distribution of molecular motors torque and nonlinear terms in
the curvature.; Comment: 13 pages in LATEX/PS, 4 figures in PS and 3 figures in GIF

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## Unusual synchronization phenomena during electrodissolution of silicon: the role of nonlinear global coupling

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 02/05/2014
Português

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491.8567%

#Nonlinear Sciences - Pattern Formation and Solitons#Nonlinear Sciences - Adaptation and Self-Organizing Systems

The photoelectrodissolution of n-type silicon constitutes a convenient model
system to study the nonlinear dynamics of oscillatory media. On the silicon
surface, a silicon oxide layer forms. In the lateral direction, the thickness
of this layer is not uniform. Rather, several spatio-temporal patterns in the
oxide layer emerge spontaneously, ranging from cluster patterns and turbulence
to quite peculiar dynamics like chimera states. Introducing a nonlinear global
coupling in the complex Ginzburg-Landau equation allows us to identify this
nonlinear coupling as the essential ingredient to describe the patterns found
in the experiments. The nonlinear global coupling is designed in such a way, as
to capture an important, experimentally observed feature: the spatially
averaged oxide-layer thickness shows nearly harmonic oscillations. Simulations
of the modified complex Ginzburg-Landau equation capture the experimental
dynamics very well.; Comment: To appear as a chapter in "Engineering of Chemical Complexity II"
(eds. A.S. Mikhailov and G.Ertl) at World Scientific in Singapore

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## Nonlinear Dynamics of Moving Curves and Surfaces: Applications to Physical Systems

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 01/04/2004
Português

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490.89445%

#Nonlinear Sciences - Pattern Formation and Solitons#Nonlinear Sciences - Exactly Solvable and Integrable Systems

The subject of moving curves (and surfaces) in three dimensional space (3-D)
is a fascinating topic not only because it represents typical nonlinear
dynamical systems in classical mechanics, but also finds important applications
in a variety of physical problems in different disciplines. Making use of the
underlying geometry, one can very often relate the associated evolution
equations to many interesting nonlinear evolution equations, including soliton
possessing nonlinear dynamical systems. Typical examples include dynamics of
filament vortices in ordinary and superfluids, spin systems, phases in
classical optics, various systems encountered in physics of soft matter, etc.
Such interrelations between geometric evolution and physical systems have
yielded considerable insight into the underlying dynamics. We present a
succinct tutorial analysis of these developments in this article, and indicate
further directions. We also point out how evolution equations for moving
surfaces are often intimately related to soliton equations in higher
dimensions.; Comment: Review article, 38 pages, 7 figs. To appear in Int. Jour. of Bif. and
Chaos

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## Sine-Gordon Solitons, Kinks and Breathers as Physical Models of Nonlinear Excitations in Living Cellular Structures

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 02/05/2013
Português

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#Quantitative Biology - Other Quantitative Biology#Nonlinear Sciences - Pattern Formation and Solitons

Nonlinear space-time dynamics, defined in terms of celebrated 'solitonic'
equations, brings indispensable tools for understanding, prediction and control
of complex behaviors in both physical and life sciences. In this paper, we
review sine-Gordon solitons, kinks and breathers as models of nonlinear
excitations in complex systems in physics and in living cellular structures,
both intra-cellular (DNA, protein folding and microtubules) and inter-cellular
(neural impulses and muscular contractions).
Key words: Sine-Gordon solitons, kinks and breathers, DNA, Protein folding,
Microtubules, Neural conduction, Muscular contraction; Comment: 55 pages, 11 figures, Latex. arXiv admin note: text overlap with
arXiv:quant-ph/9512021, arXiv:hep-ph/9505401, arXiv:nlin/0205044,
arXiv:cond-mat/0209427, arXiv:cond-mat/9906020, arXiv:patt-sol/9809011 by
other authors

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## Dynamics of Kinks in One- and Two- Dimensional Hyperbolic Models with Quasi-Discrete Nonlinearities

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 23/02/2000
Português

Relevância na Pesquisa

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#Nonlinear Sciences - Pattern Formation and Solitons#Nonlinear Sciences - Adaptation and Self-Organizing Systems

We study the evolution of fronts in the Klein-Gordon equation when the
nonlinear term is non-homogeneous. Extending previous works on homogeneous
nonlinear terms, we describe the derivation of an equation governing the front
motion, which is strongly nonlinear, and, for the two-dimensional case,
generalizes the damped Born-Infeld equation. We study the motion of one- and
two-dimensional fronts, finding that the dynamics is richer than in the
homogeneous reaction term case.

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## High-order Rogue Wave solutions for the Coupled Nonlinear Schr\"{o}dinger Equations-II

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 17/05/2015
Português

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#Nonlinear Sciences - Pattern Formation and Solitons#Nonlinear Sciences - Exactly Solvable and Integrable Systems#Physics - Atomic Physics

We study on dynamics of high-order rogue wave in two-component coupled
nonlinear Schr\"{o}dinger equations. Based on the generalized Darboux
transformation and formal series method, we obtain the high-order rogue wave
solution without the special limitation on the wave vectors. As an application,
we exhibit the first, second-order rogue wave solution and the superposition of
them by computer plotting. We find the distribution patterns for vector rogue
waves are much more abundant than the ones for scalar rogue waves, and also
different from the ones obtained with the constrain conditions on background
fields. The results further enrich and deep our realization on rogue wave
excitation dynamics in such diverse fields as Bose-Einstein condensates,
nonlinear fibers, and superfluids.; Comment: 9 pages, 7 figures

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## Soliton Dynamics in Linearly Coupled Discrete Nonlinear Schr\"odinger Equations

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 15/04/2009
Português

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486.47156%

We study soliton dynamics in a system of two linearly coupled discrete
nonlinear Schr\"odinger equations, which describe the dynamics of a
two-component Bose gas, coupled by an electromagnetic field, and confined in a
strong optical lattice. When the nonlinear coupling strengths are equal, we use
a unitary transformation to remove the linear coupling terms, and show that the
existing soliton solutions oscillate from one species to the other. When the
nonlinear coupling strengths are different, the soliton dynamics is numerically
investigated and the findings are compared to the results of an effective
two-mode model. The case of two linearly coupled Ablowitz-Ladik equations is
also investigated.; Comment: to be published in Mathematics and Computers in Simulation,
proceedings of the fifth IMACS International Conference on Nonlinear
Evolution Equations and Wave Phenomena: Computation and Theory (Athens,
Georgia - April 2007)

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## Nonlinear Waves in Lattices: Past, Present, Future

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 16/09/2010
Português

Relevância na Pesquisa

573.09504%

In the present work, we attempt a brief summary of various areas where
nonlinear waves have been emerging in the phenomenology of lattice dynamical
systems. These areas include nonlinear optics, atomic physics, mechanical
systems, electrical lattices, nonlinear metamaterials, plasma dynamics and
granular crystals. We give some of the recent developments in each one of these
areas and speculate on some of the potentially interesting directions for
future study.; Comment: 35 pages, 3 figures, brief review to appear in IMA Journal of Applied
Mathematics

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