The concept of quasi-integrability for modified non-linear Schrodinger models

We consider modifications of the nonlinear Schrodinger model (NLS) to look at the recently introduced concept of quasi-integrability. We show that such models possess an in finite number of quasi-conserved charges which present intriguing properties in relation to very specific space-time parity transformations. For the case of two-soliton solutions where the fields are eigenstates of this parity, those charges are asymptotically conserved in the scattering process of the solitons. Even though the charges vary in time their values in the far past and the far future are the same. Such results are obtained through analytical and numerical methods, and employ adaptations of algebraic techniques used in integrable field theories. Our findings may have important consequences on the applications of these models in several areas of non-linear science. We make a detailed numerical study of the modified NLS potential of the form V similar to (vertical bar psi vertical bar(2))(2+epsilon), with epsilon being a perturbation parameter. We perform numerical simulations of the scattering of solitons for this model and find a good agreement with the results predicted by the analytical considerations. Our paper shows that the quasi-integrability concepts recently proposed in the context of modifications of the sine-Gordon model remain valid for perturbations of the NLS model.

Design of laminated piezocomposite shell transducers with arbitrary fiber orientation using topology optimization approach

Sensor and actuator based on laminated piezocomposite shells have shown increasing demand in the field of smart structures. The distribution of piezoelectric material within material layers affects the performance of these structures; therefore, its amount, shape, size, placement, and polarization should be simultaneously considered in an optimization problem. In addition, previous works suggest the concept of laminated piezocomposite structure that includes fiber-reinforced composite layer can increase the performance of these piezoelectric transducers; however, the design optimization of these devices has not been fully explored yet. Thus, this work aims the development of a methodology using topology optimization techniques for static design of laminated piezocomposite shell structures by considering the optimization of piezoelectric material and polarization distributions together with the optimization of the fiber angle of the composite orthotropic layers, which is free to assume different values along the same composite layer. The finite element model is based on the laminated piezoelectric shell theory, using the degenerate three-dimensional solid approach and first-order shell theory kinematics that accounts for the transverse shear deformation and rotary inertia effects. The topology optimization formulation is implemented by combining the piezoelectric material with penalization and polarization model and the discrete material optimization, where the design variables describe the amount of piezoelectric material and polarization sign at each finite element, with the fiber angles, respectively. Three different objective functions are formulated for the design of actuators, sensors, and energy harvesters. Results of laminated piezocomposite shell transducers are presented to illustrate the method. Copyright (C) 2012 John Wiley & Sons, Ltd.

A new enrichment space for the treatment of discontinuous pressures in multi-fluid flows

In this work, a new enrichment space to accommodate jumps in the pressure field at immersed interfaces in finite element formulations, is proposed. The new enrichment adds two degrees of freedom per element that can be eliminated by means of static condensation. The new space is tested and compared with the classical P1 space and to the space proposed by Ausas et al (Comp. Meth. Appl. Mech. Eng., Vol. 199, 10191031, 2010) in several problems involving jumps in the viscosity and/or the presence of singular forces at interfaces not conforming with the element edges. The combination of this enrichment space with another enrichment that accommodates discontinuities in the pressure gradient has also been explored, exhibiting excellent results in problems involving jumps in the density or the volume forces. Copyright (c) 2011 John Wiley & Sons, Ltd.

Contributions to underwater glider path planning

[ES] La Planificación de Rutas o Caminos es un disciplina de Robótica que trata la búsqueda de caminos factibles u óptimos. Para la mayoría de vehículos y entornos, no es un problema trivial y por tanto nos encontramos con un gran diversidad de algoritmos para resolverlo, no sólo en Robótica e Inteligencia Artificial, sino también como parte de la literatura de Optimización, con Métodos Numéricos y Algoritmos Bio-inspirados, como Algoritmos Genéticos y el Algoritmo de la Colonia de Hormigas. El caso particular de escenarios de costes variables es considerablemente difícil de abordar porque el entorno en el que se mueve el vehículo cambia con el tiempo. El presente trabajo de tesis estudia este problema y propone varias soluciones prácticas para aplicaciones de Robótica Submarina.

Modellazione numerica del comportamento di una struttura in muratura

In questi ultimi anni il tema della sicurezza sismica degli edifici storici in muratura ha assunto particolare rilievo in quanto a partire soprattutto dall’ordinanza 3274 del 2003, emanata in seguito al sisma che colpì il Molise nel 2002, la normativa ha imposto un monitoraggio ed una classificazione degli edifici storici sotto tutela per quanto riguarda la vulnerabilità sismica (nel 2008, quest’anno, scade il termine per attuare quest’opera di classificazione). Si è posto per questo in modo più urgente il problema dello studio del comportamento degli edifici storici (non solo quelli che costituiscono monumento, ma anche e soprattutto quelli minori) e della loro sicurezza. Le Linee Guida di applicazione dell’Ordinanza 3274 nascono con l’intento di fornire strumenti e metodologie semplici ed efficaci per affrontare questo studio nei tempi previsti. Il problema si pone in modo particolare per le chiese, presenti in grande quantità sul territorio italiano e di cui costituiscono gran parte del patrimonio culturale; questi edifici, composti di solito da grandi elementi murari, non presentano comportamento scatolare, mancando orizzontamenti, elementi di collegamento efficace e muri di spina interni e sono particolarmente vulnerabili ad azioni sismiche; presentano inoltre un comportamento strutturale a sollecitazioni orizzontali che non può essere colto con un approccio globale basato, ad esempio, su un’analisi modale lineare: non ci sono modi di vibrare che coinvolgano una sufficiente parte di massa della struttura; si hanno valori dei coefficienti di partecipazione dei varii modi di vibrare minori del 10% (in generale molto più bassi). Per questo motivo l’esperienza e l’osservazione di casi reali suggeriscono un approccio di studio degli edifici storici sacri in muratura attraverso l’analisi della sicurezza sismica dei cosiddetti “macroelementi” in cui si può suddividere un edificio murario, i quali sono elementi che presentano un comportamento strutturale autonomo. Questo lavoro si inserisce in uno studio più ampio iniziato con una tesi di laurea dal titolo “Analisi Limite di Strutture in Muratura. Teoria e Applicazione all'Arco Trionfale” (M. Temprati), che ha studiato il comportamento dell’arco trionfale della chiesa collegiata di Santa Maria del Borgo a San Nicandro Garganico (FG). Suddividere un edificio in muratura in più elementi è il metodo proposto nelle Linee Guida, di cui si parla nel primo capitolo del presente lavoro: la vulnerabilità delle strutture può essere studiata tramite il moltiplicatore di collasso quale parametro in grado di esprimere il livello di sicurezza sismica. Nel secondo capitolo si illustra il calcolo degli indici di vulnerabilità e delle accelerazioni di danno per la chiesa di Santa Maria del Borgo, attraverso la compilazione delle schede dette “di II livello”, secondo quanto indicato nelle Linee Guida. Nel terzo capitolo viene riportato il calcolo del moltiplicatore di collasso a ribaltamento della facciata della chiesa. Su questo elemento si è incentrata l’attenzione nel presente lavoro. A causa della complessità dello schema strutturale della facciata connessa ad altri elementi dell’edificio, si è fatto uso del codice di calcolo agli elementi finiti ABAQUS. Della modellazione del materiale e del settaggio dei parametri del software si è discusso nel quarto capitolo. Nel quinto capitolo si illustra l’analisi condotta tramite ABAQUS sullo stesso schema della facciata utilizzato per il calcolo manuale nel capitolo tre: l’utilizzo combinato dell’analisi cinematica e del metodo agli elementi finiti permette per esempi semplici di convalidare i risultati ottenibili con un’analisi non-lineare agli elementi finiti e di estenderne la validità a schemi più completi e più complessi. Nel sesto capitolo infatti si riportano i risultati delle analisi condotte con ABAQUS su schemi strutturali in cui si considerano anche gli elementi connessi alla facciata. Si riesce in questo modo ad individuare con chiarezza il meccanismo di collasso di più facile attivazione per la facciata e a trarre importanti informazioni sul comportamento strutturale delle varie parti, anche in vista di un intervento di ristrutturazione e miglioramento sismico.

Computational analyses on the structure-function relation in ion channels

Ion channels are protein molecules, embedded in the lipid bilayer of the cell membranes. They act as powerful sensing elements switching chemicalphysical stimuli into ion-fluxes. At a glance, ion channels are water-filled pores, which can open and close in response to different stimuli (gating), and one once open select the permeating ion species (selectivity). They play a crucial role in several physiological functions, like nerve transmission, muscular contraction, and secretion. Besides, ion channels can be used in technological applications for different purpose (sensing of organic molecules, DNA sequencing). As a result, there is remarkable interest in understanding the molecular determinants of the channel functioning. Nowadays, both the functional and the structural characteristics of ion channels can be experimentally solved. The purpose of this thesis was to investigate the structure-function relation in ion channels, by computational techniques. Most of the analyses focused on the mechanisms of ion conduction, and the numerical methodologies to compute the channel conductance. The standard techniques for atomistic simulation of complex molecular systems (Molecular Dynamics) cannot be routinely used to calculate ion fluxes in membrane channels, because of the high computational resources needed. The main step forward of the PhD research activity was the development of a computational algorithm for the calculation of ion fluxes in protein channels. The algorithm - based on the electrodiffusion theory - is computational inexpensive, and was used for an extensive analysis on the molecular determinants of the channel conductance. The first record of ion-fluxes through a single protein channel dates back to 1976, and since then measuring the single channel conductance has become a standard experimental procedure. Chapter 1 introduces ion channels, and the experimental techniques used to measure the channel currents. The abundance of functional data (channel currents) does not match with an equal abundance of structural data. The bacterial potassium channel KcsA was the first selective ion channels to be experimentally solved (1998), and after KcsA the structures of four different potassium channels were revealed. These experimental data inspired a new era in ion channel modeling. Once the atomic structures of channels are known, it is possible to define mathematical models based on physical descriptions of the molecular systems. These physically based models can provide an atomic description of ion channel functioning, and predict the effect of structural changes. Chapter 2 introduces the computation methods used throughout the thesis to model ion channels functioning at the atomic level. In Chapter 3 and Chapter 4 the ion conduction through potassium channels is analyzed, by an approach based on the Poisson-Nernst-Planck electrodiffusion theory. In the electrodiffusion theory ion conduction is modeled by the drift-diffusion equations, thus describing the ion distributions by continuum functions. The numerical solver of the Poisson- Nernst-Planck equations was tested in the KcsA potassium channel (Chapter 3), and then used to analyze how the atomic structure of the intracellular vestibule of potassium channels affects the conductance (Chapter 4). As a major result, a correlation between the channel conductance and the potassium concentration in the intracellular vestibule emerged. The atomic structure of the channel modulates the potassium concentration in the vestibule, thus its conductance. This mechanism explains the phenotype of the BK potassium channels, a sub-family of potassium channels with high single channel conductance. The functional role of the intracellular vestibule is also the subject of Chapter 5, where the affinity of the potassium channels hEag1 (involved in tumour-cell proliferation) and hErg (important in the cardiac cycle) for several pharmaceutical drugs was compared. Both experimental measurements and molecular modeling were used in order to identify differences in the blocking mechanism of the two channels, which could be exploited in the synthesis of selective blockers. The experimental data pointed out the different role of residue mutations in the blockage of hEag1 and hErg, and the molecular modeling provided a possible explanation based on different binding sites in the intracellular vestibule. Modeling ion channels at the molecular levels relates the functioning of a channel to its atomic structure (Chapters 3-5), and can also be useful to predict the structure of ion channels (Chapter 6-7). In Chapter 6 the structure of the KcsA potassium channel depleted from potassium ions is analyzed by molecular dynamics simulations. Recently, a surprisingly high osmotic permeability of the KcsA channel was experimentally measured. All the available crystallographic structure of KcsA refers to a channel occupied by potassium ions. To conduct water molecules potassium ions must be expelled from KcsA. The structure of the potassium-depleted KcsA channel and the mechanism of water permeation are still unknown, and have been investigated by numerical simulations. Molecular dynamics of KcsA identified a possible atomic structure of the potassium-depleted KcsA channel, and a mechanism for water permeation. The depletion from potassium ions is an extreme situation for potassium channels, unlikely in physiological conditions. However, the simulation of such an extreme condition could help to identify the structural conformations, so the functional states, accessible to potassium ion channels. The last chapter of the thesis deals with the atomic structure of the !- Hemolysin channel. !-Hemolysin is the major determinant of the Staphylococcus Aureus toxicity, and is also the prototype channel for a possible usage in technological applications. The atomic structure of !- Hemolysin was revealed by X-Ray crystallography, but several experimental evidences suggest the presence of an alternative atomic structure. This alternative structure was predicted, combining experimental measurements of single channel currents and numerical simulations. This thesis is organized in two parts, in the first part an overview on ion channels and on the numerical methods adopted throughout the thesis is provided, while the second part describes the research projects tackled in the course of the PhD programme. The aim of the research activity was to relate the functional characteristics of ion channels to their atomic structure. In presenting the different research projects, the role of numerical simulations to analyze the structure-function relation in ion channels is highlighted.

Modelizzazione spazio-temporale delle dinamiche di uso del suolo ed analisi comparativa di differenti approcci predittivi. Uso integrato di SIG e telerilevamento nello studio dei processi di deforestazione nella regione La Joyanca in Peten, Guatemala

L’uso frequente dei modelli predittivi per l’analisi di sistemi complessi, naturali o artificiali, sta cambiando il tradizionale approccio alle problematiche ambientali e di rischio. Il continuo miglioramento delle capacità di elaborazione dei computer facilita l’utilizzo e la risoluzione di metodi numerici basati su una discretizzazione spazio-temporale che permette una modellizzazione predittiva di sistemi reali complessi, riproducendo l’evoluzione dei loro patterns spaziali ed calcolando il grado di precisione della simulazione. In questa tesi presentiamo una applicazione di differenti metodi predittivi (Geomatico, Reti Neurali, Land Cover Modeler e Dinamica EGO) in un’area test del Petén, Guatemala. Durante gli ultimi decenni questa regione, inclusa nella Riserva di Biosfera Maya, ha conosciuto una rapida crescita demografica ed un’incontrollata pressione sulle sue risorse naturali. L’area test puó essere suddivisa in sotto-regioni caratterizzate da differenti dinamiche di uso del suolo. Comprendere e quantificare queste differenze permette una migliore approssimazione del sistema reale; é inoltre necessario integrare tutti i parametri fisici e socio-economici, per una rappresentazione più completa della complessità dell’impatto antropico. Data l’assenza di informazioni dettagliate sull’area di studio, quasi tutti i dati sono stati ricavati dall’elaborazione di 11 immagini ETM+, TM e SPOT; abbiamo poi realizzato un’analisi multitemporale dei cambi uso del suolo passati e costruito l’input per alimentare i modelli predittivi. I dati del 1998 e 2000 sono stati usati per la fase di calibrazione per simulare i cambiamenti nella copertura terrestre del 2003, scelta come data di riferimento per la validazione dei risultati. Quest’ultima permette di evidenziare le qualità ed i limiti per ogni modello nelle differenti sub-regioni.

Calculation of the eigenfunctions of the two-group neutron diffusion equation and application to modal decomposition of BWR instabilities

In this thesis, numerical methods aiming at determining the eigenfunctions, their adjoint and the corresponding eigenvalues of the two-group neutron diffusion equations representing any heterogeneous system are investigated. First, the classical power iteration method is modified so that the calculation of modes higher than the fundamental mode is possible. Thereafter, the Explicitly-Restarted Arnoldi method, belonging to the class of Krylov subspace methods, is touched upon. Although the modified power iteration method is a computationally-expensive algorithm, its main advantage is its robustness, i.e. the method always converges to the desired eigenfunctions without any need from the user to set up any parameter in the algorithm. On the other hand, the Arnoldi method, which requires some parameters to be defined by the user, is a very efficient method for calculating eigenfunctions of large sparse system of equations with a minimum computational effort. These methods are thereafter used for off-line analysis of the stability of Boiling Water Reactors. Since several oscillation modes are usually excited (global and regional oscillations) when unstable conditions are encountered, the characterization of the stability of the reactor using for instance the Decay Ratio as a stability indicator might be difficult if the contribution from each of the modes are not separated from each other. Such a modal decomposition is applied to a stability test performed at the Swedish Ringhals-1 unit in September 2002, after the use of the Arnoldi method for pre-calculating the different eigenmodes of the neutron flux throughout the reactor. The modal decomposition clearly demonstrates the excitation of both the global and regional oscillations. Furthermore, such oscillations are found to be intermittent with a time-varying phase shift between the first and second azimuthal modes.

High-resolution simulation of stack pollutant emissions

[EN]A three-dimensional air pollution model for the short-term simulation of emission, transport and reaction of pollutants is presented. In the finite element simulation of these environmental processes over a complex terrain, a mesh generator capable of adapting itself to the topographic characteristics is essential, A local refinement of tetrahedra is used in order to capture the plume rise. Then a wind field is computed by using a mass-consistent model and perturbing its vertical component to introduce the plume rise effect. Finally, an Eulerian convection-diffusionreaction model is used to simulate the pollutant dispersion…

Simulación de la calidad del aire en la isla de Gran Canaria mediante el método de los elementos finitos y su validación con datos experimentales

[EN]Este estudio muestra una simulación 3D de la calidad del aire en la isla de Gran Canaria. Se simula el transporte difusión y reacción de los gases emitidos en dos centrales térmicas de la isla. Se presenta una estrategia de modelización y simulación mediante elementos finitos. Los resultados se comparan con datos experimentales. Se usa el método del Meccano para mallar la isla de Gran Canaria, a partir de una triangulación de la topografia de la isla. A continuación, con los datos de las estaciones de viento, se calcula un campo de viento para la zona de estudio…

Modelización de sólidos mediante estructura Octree

[EN]En este trabajo presentamos un procedimiento para la modelización de sólidos con geometríacompleja mediante una estructura octree [1]. Partiendo de una triangulación superficial del sólido, se construye una malla de hexaedros que aproxima la geometría con una precisión indicada. Para ello se emplea una división recursiva del espacio con una estructura octree. Inicialmente se lleva a cabo una traslación y escalado de la triangulación al cubo inicial [0,1]3 donde se construye el octree...

Non linear application of an in-house finite elements software

Questa tesi si pone come obiettivo l'analisi delle componenti di sollecitazione statica di un serbatoio, in acciaio API 5L X52, sottoposto a carichi di flessione e pressione interna attraverso il programma agli elementi finiti PLCd4, sviluppato presso l'International Center for Numerical Methods in Engineering (CIMNE - Barcelona). Questo tipo di analisi rientra nel progetto europeo ULCF, il cui traguardo è lo studio della fatica a bassissimo numero di cicli per strutture in acciaio. Prima di osservare la struttura completa del serbatoio è stato studiato il comportamento del materiale per implementare all'interno del programma una nuova tipologia di curva che rappresentasse al meglio l'andamento delle tensioni interne. Attraverso il lavoro di preparazione alla tesi è stato inserito all'interno del programma un algoritmo per la distribuzione delle pressioni superficiali sui corpi 3D, successivamente utilizzato per l'analisi della pressione interna nel serbatoio. Sono state effettuate analisi FEM del serbatoio in diverse configurazioni di carico ove si è cercato di modellare al meglio la struttura portante relativa al caso reale di "full scale test". Dal punto di vista analitico i risultati ottenuti sono soddisfacenti in quanto rispecchiano un corretto comportamento del serbatoio in condizioni di pressioni molto elevate e confermano la bontà del programma nell'analisi computazionale.

Resonances in the two centers Coulomb system

In this work we investigate the existence of resonances for two-centers Coulomb systems with arbitrary charges in two and three dimensions, defining them in terms of generalized complex eigenvalues of a non-selfadjoint deformation of the two-center Schrödinger operator. After giving a description of the bifurcation of the classical system for positive energies, we construct the resolvent kernel of the operators and we prove that they can be extended analytically to the second Riemann sheet. The resonances are then defined and studied with numerical methods and perturbation theory.

Automotive diesel engine transient operation: modeling, optimization and control

Traditionally, the study of internal combustion engines operation has focused on the steady-state performance. However, the daily driving schedule of automotive engines is inherently related to unsteady conditions. There are various operating conditions experienced by (diesel) engines that can be classified as transient. Besides the variation of the engine operating point, in terms of engine speed and torque, also the warm up phase can be considered as a transient condition. Chapter 2 has to do with this thermal transient condition; more precisely the main issue is the performance of a Selective Catalytic Reduction (SCR) system during cold start and warm up phases of the engine. The proposal of the underlying work is to investigate and identify optimal exhaust line heating strategies, to provide a fast activation of the catalytic reactions on SCR. Chapters 3 and 4 focus the attention on the dynamic behavior of the engine, when considering typical driving conditions. The common approach to dynamic optimization involves the solution of a single optimal-control problem. However, this approach requires the availability of models that are valid throughout the whole engine operating range and actuator ranges. In addition, the result of the optimization is meaningful only if the model is very accurate. Chapter 3 proposes a methodology to circumvent those demanding requirements: an iteration between transient measurements to refine a purpose-built model and a dynamic optimization which is constrained to the model validity region. Moreover all numerical methods required to implement this procedure are presented. Chapter 4 proposes an approach to derive a transient feedforward control system in an automated way. It relies on optimal control theory to solve a dynamic optimization problem for fast transients. From the optimal solutions, the relevant information is extracted and stored in maps spanned by the engine speed and the torque gradient.

Periodicities in the Hodgkin-Huxley model and versions of this model with stochastic input

A field of computational neuroscience develops mathematical models to describe neuronal systems. The aim is to better understand the nervous system. Historically, the integrate-and-fire model, developed by Lapique in 1907, was the first model describing a neuron. In 1952 Hodgkin and Huxley [8] described the so called Hodgkin-Huxley model in the article “A Quantitative Description of Membrane Current and Its Application to Conduction and Excitation in Nerve”. The Hodgkin-Huxley model is one of the most successful and widely-used biological neuron models. Based on experimental data from the squid giant axon, Hodgkin and Huxley developed their mathematical model as a four-dimensional system of first-order ordinary differential equations. One of these equations characterizes the membrane potential as a process in time, whereas the other three equations depict the opening and closing state of sodium and potassium ion channels. The membrane potential is proportional to the sum of ionic current flowing across the membrane and an externally applied current. For various types of external input the membrane potential behaves differently. This thesis considers the following three types of input: (i) Rinzel and Miller [15] calculated an interval of amplitudes for a constant applied current, where the membrane potential is repetitively spiking; (ii) Aihara, Matsumoto and Ikegaya [1] said that dependent on the amplitude and the frequency of a periodic applied current the membrane potential responds periodically; (iii) Izhikevich [12] stated that brief pulses of positive and negative current with different amplitudes and frequencies can lead to a periodic response of the membrane potential. In chapter 1 the Hodgkin-Huxley model is introduced according to Izhikevich [12]. Besides the definition of the model, several biological and physiological notes are made, and further concepts are described by examples. Moreover, the numerical methods to solve the equations of the Hodgkin-Huxley model are presented which were used for the computer simulations in chapter 2 and chapter 3. In chapter 2 the statements for the three different inputs (i), (ii) and (iii) will be verified, and periodic behavior for the inputs (ii) and (iii) will be investigated. In chapter 3 the inputs are embedded in an Ornstein-Uhlenbeck process to see the influence of noise on the results of chapter 2.