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

Togashi, Yuichi; Mikhailov, Alexander S.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
55.6%
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.

Fluctuations of fish populations and the magnifying effects of fishing

Shelton, Andrew O.; Mangel, Marc
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
45.71%
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...

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

Valenza, Gaetano; Citi, Luca; Barbieri, Riccardo
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
45.74%
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.

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

Sugiyama, Masahiro, Ph. D. Massachusetts Institute of Technology
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 245 p.
Português
Relevância na Pesquisa
45.71%
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...

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

Dreischuh, Alexander; Neshev, Dragomir; Kolev, Vesselin Z; Saltiel, Solomon; Samoc, Marek; Krolikowski, Wieslaw; Kivshar, Yuri
Fonte: Universidade Nacional da Austrália Publicador: Universidade Nacional da Austrália
Tipo: Journal article; Published Version Formato: 15 pages
Português
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45.69%
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.

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

Gentilini, Silvia; Braidotti, Maria Chiara; Marcucci, Giulia; DelRe, Eugenio; Conti, Claudio
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 04/08/2015 Português
Relevância na Pesquisa
45.68%
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...

Quasiclassical Calculations of Wigner Functions in Nonlinear Beam Dynamics

Fedorova, Antonina N.; Zeitlin, Michael G.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 02/06/2001 Português
Relevância na Pesquisa
55.6%
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

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

Medvedev, M. V.; Diamond, P. H.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 30/12/1996 Português
Relevância na Pesquisa
55.67%
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)

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

Medvedev, M. V.; Shevchenko, V. I.; Diamond, P. H.; Galinsky, V. L.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 30/12/1996 Português
Relevância na Pesquisa
55.68%
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)

Dissipative Dynamics of Collisionless Nonlinear Alfven Wave Trains

Medvedev, M. V.; Diamond, P. H.; Shevchenko, V. I.; Galinsky, V. L.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 25/07/1997 Português
Relevância na Pesquisa
45.7%
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

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

Lizier, Joseph T.; Prokopenko, Mikhail; Zomaya, Albert Y.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
45.69%
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...

Local Analysis of Nonlinear RMS Envelope Dynamics

Fedorova, Antonina N.; Zeitlin, Michael G.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 13/08/2000 Português
Relevância na Pesquisa
55.58%
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

Dynamics of Immobilized Flagella

Fry, D.; Hutchings, N.; Ludu, A.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
45.7%
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

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

Schmidt, Lennart; Schönleber, Konrad; García-Morales, Vladimir; Krischer, Katharina
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 02/05/2014 Português
Relevância na Pesquisa
45.71%
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

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

Murugesh, S.; Lakshmanan, M.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 01/04/2004 Português
Relevância na Pesquisa
45.71%
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

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

Ivancevic, Vladimir G.; Ivancevic, Tijana T.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 02/05/2013 Português
Relevância na Pesquisa
55.6%
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

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

Rotstein, Horacio G.; Zhabotinsky, Anatol; Epstein, Irving
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 23/02/2000 Português
Relevância na Pesquisa
45.67%
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.

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

Zhao, Li-Chen; Guo, Boling; Ling, Liming
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 17/05/2015 Português
Relevância na Pesquisa
45.67%
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

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

Trombettoni, A.; Nistazakis, H. E.; Rapti, Z.; Frantzeskakis, D. J.; Kevrekidis, P. G.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 15/04/2009 Português
Relevância na Pesquisa
45.67%
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)

Nonlinear Waves in Lattices: Past, Present, Future

Kevrekidis, P. G.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 16/09/2010 Português
Relevância na Pesquisa
55.57%
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