Semi-algebraic methods for symbolic analysis of complex reaction networks

The identification of chemical mechanism that can exhibit oscillatory phenomena in reaction networks are currently of intense interest. In particular, the parametric question of the existence of Hopf bifurcations has gained increasing popularity due to its relation to the oscillatory behavior around the fixed points. However, the detection of oscillations in high-dimensional systems and systems with constraints by the available symbolic methods has proven to be difficult. The development of new efficient methods are therefore required to tackle the complexity caused by the high-dimensionality and non-linearity of these systems. In this thesis, we mainly present efficient algorithmic methods to detect Hopf bifurcation fixed points in (bio)-chemical reaction networks with symbolic rate constants, thereby yielding information about their oscillatory behavior of the networks. The methods use the representations of the systems on convex coordinates that arise from stoichiometric network analysis. One of the methods called HoCoQ reduces the problem of determining the existence of Hopf bifurcation fixed points to a first-order formula over the ordered field of the reals that can then be solved using computational-logic packages. The second method called HoCaT uses ideas from tropical geometry to formulate a more efficient method that is incomplete in theory but worked very well for the attempted high-dimensional models involving more than 20 chemical species. The instability of reaction networks may lead to the oscillatory behaviour. Therefore, we investigate some criterions for their stability using convex coordinates and quantifier elimination techniques. We also study Muldowney's extension of the classical Bendixson-Dulac criterion for excluding periodic orbits to higher dimensions for polynomial vector fields and we discuss the use of simple conservation constraints and the use of parametric constraints for describing simple convex polytopes on which periodic orbits can be excluded by Muldowney's criteria. All developed algorithms have been integrated into a common software framework called PoCaB (platform to explore bio- chemical reaction networks by algebraic methods) allowing for automated computation workflows from the problem descriptions. PoCaB also contains a database for the algebraic entities computed from the models of chemical reaction networks.

Steady periodic water waves with constant vorticity: regularity and local bifurcation

This paper studies periodic traveling gravity waves at the free surface of water in a flow of constant vorticity over a flat bed. Using conformal mappings the free-boundary problem is transformed into a quasilinear pseudodifferential equation for a periodic function of one variable. The new formulation leads to a regularity result and, by use of bifurcation theory, to the existence of waves of small amplitude even in the presence of stagnation points in the flow.

The problem of two fixed centers: bifurcation diagram for positive energies

We give a comprehensive analysis of the Euler-Jacobi problem of motion in the field of two fixed centers with arbitrary relative strength and for positive values of the energy. These systems represent nontrivial examples of integrable dynamics and are analysed from the point of view of the energy-momentum mapping from the phase space to the space of the integration constants. In this setting, we describe the structure of the scattering trajectories in phase space and derive an explicit description of the bifurcation diagram, i.e., the set of critical value of the energy-momentum map.

ENHANCING MULTISCALE FRACTAL DESCRIPTORS USING FUNCTIONAL DATA ANALYSIS

This work presents a novel approach in order to increase the recognition power of Multiscale Fractal Dimension (MFD) techniques, when applied to image classification. The proposal uses Functional Data Analysis (FDA) with the aim of enhancing the MFD technique precision achieving a more representative descriptors vector, capable of recognizing and characterizing more precisely objects in an image. FDA is applied to signatures extracted by using the Bouligand-Minkowsky MFD technique in the generation of a descriptors vector from them. For the evaluation of the obtained improvement, an experiment using two datasets of objects was carried out. A dataset was used of characters shapes (26 characters of the Latin alphabet) carrying different levels of controlled noise and a dataset of fish images contours. A comparison with the use of the well-known methods of Fourier and wavelets descriptors was performed with the aim of verifying the performance of FDA method. The descriptor vectors were submitted to Linear Discriminant Analysis (LDA) classification method and we compared the correctness rate in the classification process among the descriptors methods. The results demonstrate that FDA overcomes the literature methods (Fourier and wavelets) in the processing of information extracted from the MFD signature. In this way, the proposed method can be considered as an interesting choice for pattern recognition and image classification using fractal analysis.

Stability and Hopf bifurcation in an hexagonal governor system

In this paper we study the Lyapunov stability and the Hopf bifurcation in a system coupling an hexagonal centrifugal governor with a steam engine. Here are given sufficient conditions for the stability of the equilibrium state and of the bifurcating periodic orbit. These conditions are expressed in terms of the physical parameters of the system, and hold for parameters outside a variety of codimension two. (C) 2007 Elsevier Ltd. All rights reserved.

Analysis of spherical indentation of superelastic shape memory alloys

Dimensional analysis and the finite element method are applied in this paper to study spherical indentation of superelastic shape memory alloys. The scaling relationships derived from dimensional analysis bridge the indentation response and the mechanical properties of a superelastic shape memory alloy. Several key variables of a superelastic indentation curve are revealed and examined. We prove that the bifurcation force in a superelastic indentation curve only relies on the forward transformation stress and the elastic properties of the initial austenite; and the return force in a superelastic indentation curve only relies on the reverse transformation stress and the elastic properties of the initial austenite. Furthermore, the dimensionless functions to determine the bifurcation force and the return force are proved to be identical. These results not only enhance our understanding of spherical indentation of superelastic shape memory alloys, but also provide the theoretical basis for developing a practicable method to calibrate the mechanical properties of a superelastic material from the spherical indentation test.

Bifurcation of limit cycles from an n-dimensional linear center inside a class of piecewise linear differential systems

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

On local analysis of oscillations of a non-ideal and non-linear mechanical model

It is of major importance to consider non-ideal energy sources in engineering problems. They act on an oscillating system and at the same time experience a reciprocal action from the system. Here, a non-ideal system is studied. In this system, the interaction between source energy and motion is accomplished through a special kind of friction. Results about the stability and instability of the equilibrium point of this system are obtained. Moreover, its bifurcation curves are determined. Hopf bifurcations are found in the set of parameters of the oscillating system.

Reversible equivariant Hopf bifurcation

In this paper we study codimension-one Hopf bifurcation from symmetric equilibrium points in reversible equivariant vector fields. Such bifurcations are characterized by a doubly degenerate pair of purely imaginary eigenvalues of the linearization of the vector field at the equilibrium point. The eigenvalue movements near such a degeneracy typically follow one of three scenarios: splitting (from two pairs of imaginary eigenvalues to a quadruplet on the complex plane), passing (on the imaginary axis), or crossing (a quadruplet crossing the imaginary axis). We give a complete description of the behaviour of reversible periodic orbits in the vicinity of such a bifurcation point. For non-reversible periodic solutions. in the case of Hopf bifurcation with crossing eigenvalues. we obtain a generalization of the equivariant Hopf Theorem.

On bifurcation and symmetry of solutions of symmetric nonlinear equations with odd-harmonic forcings

In this work we study existence, bifurcation, and symmetries of small solutions of the nonlinear equation Lx = N(x, p, epsilon) + mu f, which is supposed to be equivariant under the action of a group OHm, and where f is supposed to be OHm-invariant. We assume that L is a linear operator and N(., p, epsilon) is a nonlinear operator, both defined in a Banach space X, with values in a Banach space Z, and p, mu, and epsilon are small real parameters. Under certain conditions we show the existence of symmetric solutions and under additional conditions we prove that these are the only feasible solutions. Some examples of nonlinear ordinary and partial differential equations are analyzed. (C) 1995 Academic Press, Inc.

Behavioural Analysis of a Nonlinear Mechanical System Using Transient Trajectories

This work aims at a better comprehension of the features of the solution surface of a dynamical system presenting a numerical procedure based on transient trajectories. For a given set of initial conditions an analysis is made, similar to that of a return map, looking for the new configuration of this set in the first Poincaré sections. The mentioned set of I.C. will result in a curve that can be fitted by a polynomial, i.e. an analytical expression that will be called initial function in the undamped case and transient function in the damped situation. Thus, it is possible to identify using analytical methods the main stable regions of the phase portrait without a long computational time, making easier a global comprehension of the nonlinear dynamics and the corresponding stability analysis of its solutions. This strategy allows foreseeing the dynamic behavior of the system close to the region of fundamental resonance, providing a better visualization of the structure of its phase portrait. The application chosen to present this methodology is a mechanical pendulum driven through a crankshaft that moves horizontally its suspension point.

Nonlinear dynamical analysis of an aeroelastic system with multi-segmented moment in the pitch degree-of-freedom

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Characterization of grazing bifurcation in airfoils with control surface freeplay nonlinearity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Chaos control and sensitivity analysis of a double pendulum arm excited by an RLC circuit based nonlinear shaker

In this paper the dynamical interactions of a double pendulum arm and an electromechanical shaker is investigated. The double pendulum is a three degree of freedom system coupled to an RLC circuit based nonlinear shaker through a magnetic field, and the capacitor voltage is a nonlinear function of the instantaneous electric charge. Numerical simulations show the existence of chaotic behavior for some regions in the parameter space and this behaviour is characterized by power spectral density and Lyapunov exponents. The bifurcation diagram is constructed to explore the qualitative behaviour of the system. This kind of electromechanical system is frequently found in robotic systems, and in order to suppress the chaotic motion, the State-Dependent Riccati Equation (SDRE) control and the Nonlinear Saturation control (NSC) techniques are analyzed. The robustness of these two controllers is tested by a sensitivity analysis to parametric uncertainties.

Twelve-month clinical outcomes after coronary stenting with the Genous Bio-engineered R Stent in patients with a bifurcation lesion: from the e-HEALING (Healthy Endothelial Accelerated Lining Inhibits Neointimal Growth) registry

Background The e-Healthy Endothelial Accelerated Lining Inhibits Neointimal Growth (e-HEALING) registry was designed to capture clinical data on the use of the endothelial progenitor cell capture stent (ECS) in routine clinical practice. In this analysis, we investigated the 12-month clinical outcomes in patients treated with an ECS for a bifurcation lesion. Methods The worldwide, prospective, nonrandomized e-HEALING registry aimed to enrol 5000 patients treated for coronary artery disease with one or more ECS between October 2005 and October 2007. Clinical follow-up was obtained at 1, 6, and 12 months. The primary endpoint was target vessel failure (TVF), defined as the composite of cardiac death, myocardial infarction, and target vessel revascularization at 12 months. Results A total of 573 patients were treated for at least one bifurcation lesion and were assessed in the current analysis. Baseline characteristics showed a median age of 65 years; 21% were diabetic patients and 36% had unstable angina. A total of 63% of the bifurcation lesions were located in the left artery descending and the mean stent length was 20.7 +/- 12.6 mm. At 12 months, TVF was 12.7% and target lesion revascularization was 7.5%. Definite or probable stent thrombosis occurred in 1.7% of the patients. Moreover, one or more stents per lesion [hazard ratio (HR): 2.79, 95% confidence interval (CI): 1.60-4.86, P < 0.001], predilatation (HR: 0.39, 95% CI: 0.17-0.87, P = 0.023), and lesions located in the right coronary artery (HR: 4.56, 95% CI: 1.07-19.5, P = 0.041) were independent predictors of TVF. Conclusion In the e-HEALING registry, coronary bifurcation stenting with the ECS results in favorable clinical outcomes and low incidences of repeat revascularization and stent thrombosis. Coron Artery Dis 23:201-207 (C) 2012 Wolters Kluwer Health vertical bar Lippincott Williams & Wilkins.