Dynamics of gene expression in an artificial genome

Complex systems techniques provide a powerful tool to study the emergent properties of networks of interacting genes. In this study we extract models of genetic regulatory networks from an artificial genome, represented by a sequence of nucleotides, and analyse how variations in the connectivity and degree of inhibition of the extracted networks affects the resulting classes of behaviours. For low connectivity systems were found to be very stable. Only with higher connectivity was a significant occurrence of chaos found. Most interestingly, the peak in occurrence of chaos occurs perched on the edge of a phase transition in the occurrence of attractors.

Approximating differentiable relationships between delay embedded dynamical systems with radical basis functions

This thesis is about the study of relationships between experimental dynamical systems. The basic approach is to fit radial basis function maps between time delay embeddings of manifolds. We have shown that under certain conditions these maps are generically diffeomorphisms, and can be analysed to determine whether or not the manifolds in question are diffeomorphically related to each other. If not, a study of the distribution of errors may provide information about the lack of equivalence between the two. The method has applications wherever two or more sensors are used to measure a single system, or where a single sensor can respond on more than one time scale: their respective time series can be tested to determine whether or not they are coupled, and to what degree. One application which we have explored is the determination of a minimum embedding dimension for dynamical system reconstruction. In this special case the diffeomorphism in question is closely related to the predictor for the time series itself. Linear transformations of delay embedded manifolds can also be shown to have nonlinear inverses under the right conditions, and we have used radial basis functions to approximate these inverse maps in a variety of contexts. This method is particularly useful when the linear transformation corresponds to the delay embedding of a finite impulse response filtered time series. One application of fitting an inverse to this linear map is the detection of periodic orbits in chaotic attractors, using suitably tuned filters. This method has also been used to separate signals with known bandwidths from deterministic noise, by tuning a filter to stop the signal and then recovering the chaos with the nonlinear inverse. The method may have applications to the cancellation of noise generated by mechanical or electrical systems. In the course of this research a sophisticated piece of software has been developed. The program allows the construction of a hierarchy of delay embeddings from scalar and multi-valued time series. The embedded objects can be analysed graphically, and radial basis function maps can be fitted between them asynchronously, in parallel, on a multi-processor machine. In addition to a graphical user interface, the program can be driven by a batch mode command language, incorporating the concept of parallel and sequential instruction groups and enabling complex sequences of experiments to be performed in parallel in a resource-efficient manner.

All-fiber-integrated soliton-similariton laser with in-line fiber filter

We demonstrate an all-fiber-integrated Er-doped fiber laser operating in the soliton-similariton mode-locking regime. In the similariton part of the cavity, a self-similarly evolving parabolic pulse with highly linear chirp propagates in the presence of normal dispersion. Following an in-line fiber-based birefringent filter, the pulse evolves into a soliton in the part of the cavity with anomalous dispersion. The similariton and the soliton pulses are dechirped to 75.5 and 167.2 fs, respectively, outside of the cavity. Mode-locked operation is very robust, owing to the influence of the two similariton and soliton attractors that predominate each half of the laser cavity. The experimental results are supported with numerical simulations, which provide good agreement.

Spiral attractor created by vector solitons

Mode-locked lasers emitting a train of femtosecond pulses called dissipative solitons are an enabling technology for metrology, high-resolution spectroscopy, fibre optic communications, nano-optics and many other fields of science and applications. Recently, the vector nature of dissipative solitons has been exploited to demonstrate mode locked lasing with both locked and rapidly evolving states of polarisation. Here, for an erbium-doped fibre laser mode locked with carbon nanotubes, we demonstrate the first experimental and theoretical evidence of a new class of slowly evolving vector solitons characterized by a double-scroll chaotic polarisation attractor substantially different from Lorenz, Rössler and Ikeda strange attractors. The underlying physics comprises a long time scale coherent coupling of two polarisation modes. The observed phenomena, apart from the fundamental interest, provide a base for advances in secure communications, trapping and manipulation of atoms and nanoparticles, control of magnetisation in data storage devices and many other areas. © 2014 CIOMP. All rights reserved.

Neural Control of Chaos and Aplications

Signal processing is an important topic in technological research today. In the areas of nonlinear dynamics search, the endeavor to control or order chaos is an issue that has received increasing attention over the last few years. Increasing interest in neural networks composed of simple processing elements (neurons) has led to widespread use of such networks to control dynamic systems learning. This paper presents backpropagation-based neural network architecture that can be used as a controller to stabilize unsteady periodic orbits. It also presents a neural network-based method for transferring the dynamics among attractors, leading to more efficient system control. The procedure can be applied to every point of the basin, no matter how far away from the attractor they are. Finally, this paper shows how two mixed chaotic signals can be controlled using a backpropagation neural network as a filter to separate and control both signals at the same time. The neural network provides more effective control, overcoming the problems that arise with control feedback methods. Control is more effective because it can be applied to the system at any point, even if it is moving away from the target state, which prevents waiting times. Also control can be applied even if there is little information about the system and remains stable longer even in the presence of random dynamic noise.

Vector solitons in harmonic mode-locked erbium-doped fiber lasers

We report experimental study of vector solitons for the fundamental and harmonic mode-locked operation in erbiumdoper fiber lasers with carbon nanotubes based saturable absorbers and anomalous dispersion cavities. We measure evolution of the output pulses polarization and demonstrate vector solitons with various polarization attractors, including locked polarization, periodic polarization switching, and polarization precession.

Parabolic similaritons in optical fibres

Recent developments in nonlinear optics have brought to the fore of intensive research an interesting class of pulses with a parabolic intensity profile and a linear instantaneous frequency shift or chirp. Parabolic pulses propagate in optical fibres with normal group-velocity dispersion in a self-similar manner, holding certain relations (scaling) between pulse power, duration and chirp parameter, and can tolerate strong nonlinearity without distortion or wave breaking.  These solutions, which have been dubbed similaritons, were demonstrated theoretically and experimentally in fiber amplifiers in 2000. Similaritons in fiber amplifiers are, along with solitons in passive fibres, the most well-known classes of nonlinear attractors for pulse propagation in optical fibre, so they take on major fundamental importance. The unique properties of parabolic similaritons have stimulated numerous applications in nonlinear optics, ranging from ultrashort high-power pulse generation to highly coherent continuum sources and to optical nonlinear processing of telecommunication signals.

Parabolic similaritons in optical fibres

Recent developments in nonlinear optics have brought to the fore of intensive research an interesting class of pulses with a parabolic intensity profile and a linear instantaneous frequency shift or chirp. Parabolic pulses propagate in optical fibres with normal group-velocity dispersion in a self-similar manner, holding certain relations (scaling) between pulse power, duration and chirp parameter, and can tolerate strong nonlinearity without distortion or wave breaking. These solutions, which have been dubbed similaritons, were demonstrated theoretically and experimentally in fibre amplifiers in 2000. Similaritons in fibre amplifiers are, along with solitons in passive fibres, the most well-known classes of nonlinear attractors for pulse propagation in optical fibre, so they take on major fundamental importance. The unique properties of parabolic similaritons have stimulated numerous applications in nonlinear optics, ranging from ultrashort high-power pulse generation to highly coherent continuum sources and to optical nonlinear processing of telecommunication signals. In this work, we review the physics underlying the generation of parabolic similaritons as well as recent results obtained in a wide range of experimental configurations.

Strongly localized moving discrete dissipative breather-solitons in Kerr nonlinear media supported by intrinsic gain

We investigate the mobility of nonlinear localized modes in a generalized discrete Ginzburg-Landau-type model, describing a one-dimensional waveguide array in an active Kerr medium with intrinsic, saturable gain and damping. It is shown that exponentially localized, traveling discrete dissipative breather-solitons may exist as stable attractors supported only by intrinsic properties of the medium, i.e., in the absence of any external field or symmetry-breaking perturbations. Through an interplay by the gain and damping effects, the moving soliton may overcome the Peierls-Nabarro barrier, present in the corresponding conservative system, by self-induced time-periodic oscillations of its power (norm) and energy (Hamiltonian), yielding exponential decays to zero with different rates in the forward and backward directions. In certain parameter windows, bistability appears between fast modes with small oscillations and slower, large-oscillation modes. The velocities and the oscillation periods are typically related by lattice commensurability and exhibit period-doubling bifurcations to chaotically "walking" modes under parameter variations. If the model is augmented by intersite Kerr nonlinearity, thereby reducing the Peierls-Nabarro barrier of the conservative system, the existence regime for moving solitons increases considerably, and a richer scenario appears including Hopf bifurcations to incommensurately moving solutions and phase-locking intervals. Stable moving breathers also survive in the presence of weak disorder. © 2014 American Physical Society.

Computation of rare transitions in the barotropic quasi-geostrophic equations

We investigate the theoretical and numerical computation of rare transitions in simple geophysical turbulent models. We consider the barotropic quasi-geostrophic and two-dimensional Navier–Stokes equations in regimes where bistability between two coexisting large-scale attractors exist. By means of large deviations and instanton theory with the use of an Onsager–Machlup path integral formalism for the transition probability, we show how one can directly compute the most probable transition path between two coexisting attractors analytically in an equilibrium (Langevin) framework and numerically otherWe adapt a class of numerical optimization algorithms known as minimum action methods to simple geophysical turbulent models. We show that by numerically minimizing an appropriate action functional in a large deviation limit, one can predict the most likely transition path for a rare transition between two states. By considering examples where theoretical predictions can be made, we show that the minimum action method successfully predicts the most likely transition path. Finally, we discuss the application and extension of such numerical optimization schemes to the computation of rare transitions observed in direct numerical simulations and experiments and to other, more complex, turbulent systems.

Langevin dynamics, large deviations and instantons for the quasi-geostrophic model and two-dimensional Euler equations

We investigate a class of simple models for Langevin dynamics of turbulent flows, including the one-layer quasi-geostrophic equation and the two-dimensional Euler equations. Starting from a path integral representation of the transition probability, we compute the most probable fluctuation paths from one attractor to any state within its basin of attraction. We prove that such fluctuation paths are the time reversed trajectories of the relaxation paths for a corresponding dual dynamics, which are also within the framework of quasi-geostrophic Langevin dynamics. Cases with or without detailed balance are studied. We discuss a specific example for which the stationary measure displays either a second order (continuous) or a first order (discontinuous) phase transition and a tricritical point. In situations where a first order phase transition is observed, the dynamics are bistable. Then, the transition paths between two coexisting attractors are instantons (fluctuation paths from an attractor to a saddle), which are related to the relaxation paths of the corresponding dual dynamics. For this example, we show how one can analytically determine the instantons and compute the transition probabilities for rare transitions between two attractors.

Nemlineáris dinamika klasszikus növekedési modellekben (Nonlinear dynamics in classical economic growth models)

Ebben a tanulmányban a klasszikus Harrod növekedési modellt nemlineáris kiterjesztéssel, keynesi és schumpeteri tradíciók bevezetésével reprezentatív ügynök modellbe alakítjuk. A híres Lucas kritika igazolásaként megmutatjuk, hogy az intrinsic gazdasági növekedési ütemek trajektóriái vagy egy turbulens káoszba szóródnak szét, vagy egy nagyméretű rendhez vezetnek, ami elsődlegesen a megfelelő fogyasztási függvény típusától függ, s bizonyos paraméterek piaci értékei, pedig csak másodlagos szerepet játszanak. A másik meglepő eredmény empirikus, ami szerint külkereskedelmi többlet, a hazai valuta bizonyos devizapiaci értékei mellett, különös attraktorokat generálhat. _____ In this paper the classical Harrodian growth model is transformed into a representative agent model by its nonlinear extensions and the Keynesian and Schumpeterian traditions. For the proof of the celebrated Lucas critique it is shown that the trajectories of intrinsic economic growth rates either are scattered into a turbulent chaos or lead to a large scale order. It depends on the type of the appropriate consumption function, and the market values of some parameters are playing only secondary role.Another surprising result is empirical: the international trade su±cit may generate strange attractors under some exchange rate values.

Temporal scaling of optical rogue waves in unidirectional ring fiber laser

A fiber mode-lock laser allows generation of the optical rogue wave (ORW) at different time scales. The criteria for distinguishing between them is a comparison of the event lifetime with the main characteristic time of the system. The characteristic time can be estimated from the decay of an autocorrelation function (AF). Thus, in comparison with AF characteristic time, fast optical rogue wave (FORW) events have duration less than the AF decay time and it appeared due to pulse-pulse interaction and nonlinear pulses dynamics. While slow optical rogue wave (SORW) have a duration much more longer than the decay time of the AF which it papered due to hopping between different attractors. Switching between regimes can be managed by change the artificial birefringence that induced in a laser cavity. For understanding the role playing by the periodical amplification and the resonator, we have performed an unidirectional fiber laser experiments without a saturable absorber. This laser experiment allowed to generate of most of the RW patterns which were either observed experimentally or predicted theoretically. In this way, we have observed the generation of an FORW along with SORW under similar conditions. Most of the patterns were found to be mutually exclusive which means that only one RW mechanism was realized in each regime of generation.

Aportes de las teorías sociológicas a la discusión de la ontología. Los casos de Luhmann, Habermas y Latour

En este trabajo se discuten los aportes de la teoría sociológica contemporánea al debate filosófico y científico de la ontología, para ello son cotejados los componentes ontológicos de la Teoría General de Sistemas Sociales de Niklas Luhmann, lla Teoría de la Acción Comunicativa de Jürgen Habermas y la Actor-Network Theory de Bruno Latour.

Vector self-pulsing in erbium-doped fiber lasers

Insight into instabilities of fiber laser regimes leading to complex self-pulsing operations is an opportunity to unlock the high power and dynamic operation tunability of lasers. Though many models have been suggested, there is no complete covering of self-pulsing complexity observed experimentally. Here, I further generalized our previous vector model of erbium-doped fiber laser and, for the first time, to the best of my knowledge, map tunability of complex vector self-pulsing on Poincare sphere (limit cycles and double scroll polarization attractors) for laser parameters, e.g., power, ellipticity of the pump wave, and in-cavity birefringence. Analysis validated by extensive numerical simulations demonstrates good correspondence to the experimental results on complex self-pulsing regimes obtained by many authors during the last 20 years.