Computational simulation of the flow-induced vibration of a circular cylinder subjected to wake interference

In this work, we considered the flow around two circular cylinders of equal diameter placed in tandem with respect to the incident uniform flow. The upstream cylinder was fixed and the downstream cylinder was completely free to move in the cross-stream direction, with no spring or damper attached to it. The centre-to-centre distance between the cylinders was four diameters, and the Reynolds number was varied from 100 to 645. We performed two- and three-dimensional simulations of this flow using a Spectral/hp element method to discretise the flow equations, coupled to a simple Newmark integration routine that solves the equation of the dynamics of the cylinder. The differences of the behaviours observed in the two- and three-dimensional simulations are highlighted and the data is analysed under the light of previously published experimental results obtained for higher Reynolds numbers.

Topics in geometry, analysis and inverse problems

The thesis consists of three independent parts. Part I: Polynomial amoebas We study the amoeba of a polynomial, as de ned by Gelfand, Kapranov and Zelevinsky. A central role in the treatment is played by a certain convex function which is linear in each complement component of the amoeba, which we call the Ronkin function. This function is used in two di erent ways. First, we use it to construct a polyhedral complex, which we call a spine, approximating the amoeba. Second, the Monge-Ampere measure of the Ronkin function has interesting properties which we explore. This measure can be used to derive an upper bound on the area of an amoeba in two dimensions. We also obtain results on the number of complement components of an amoeba, and consider possible extensions of the theory to varieties of codimension higher than 1. Part II: Differential equations in the complex plane We consider polynomials in one complex variable arising as eigenfunctions of certain differential operators, and obtain results on the distribution of their zeros. We show that in the limit when the degree of the polynomial approaches innity, its zeros are distributed according to a certain probability measure. This measure has its support on the union of nitely many curve segments, and can be characterized by a simple condition on its Cauchy transform. Part III: Radon transforms and tomography This part is concerned with different weighted Radon transforms in two dimensions, in particular the problem of inverting such transforms. We obtain stability results of this inverse problem for rather general classes of weights, including weights of attenuation type with data acquisition limited to a 180 degrees range of angles. We also derive an inversion formula for the exponential Radon transform, with the same restriction on the angle.

Computational chemistry studies of UV induced processes in human skin

This thesis presents and uses the techniques of computational chemistry to explore two different processes induced in human skin by ultraviolet light. The first is the transformation of urocanic acid into a immunosuppressing agent, and the other is the enzymatic action of the 8-oxoguanine glycosylase enzyme. The photochemistry of urocanic acid is investigated by time-dependent density functional theory. Vertical absorption spectra of the molecule in different forms and environments is assigned and candidate states for the photochemistry at different wavelengths are identified. Molecular dynamics simulations of urocanic acid in gas phase and aqueous solution reveals considerable flexibility under experimental conditions, particularly for for the cis isomer where competition between intra- and inter-molecular interactions increases flexibility. A model to explain the observed gas phase photochemistry of urocanic acid is developed and it is shown that a reinterpretation in terms of a mixture between isomers significantly enhances the agreement between theory and experiment , and resolves several peculiarities in the spectrum. A model for the photochemistry in the aqueous phase of urocanic acid is then developed, in which two excited states governs the efficiency of photoisomerization. The point of entrance into a conical intersection seam is shown to explain the wavelength dependence of photoisomerization quantum yield. Finally some mechanistic aspects of the DNA repair enzyme 8-oxoguanine glycosylase is investigated with density functional theory. It is found that the critical amino acid of the active site can provide catalytic power in several different manners, and that a recent proposal involving a SN1 type of mechanism seems the most efficient one.

A variational approach to 3D cylindrical geometry reconstruction from multiple views

[EN] In this paper we present a variational technique for the reconstruction of 3D cylindrical surfaces. Roughly speaking by a cylindrical surface we mean a surface that can be parameterized using the projection on a cylinder in terms of two coordinates, representing the displacement and angle in a cylindrical coordinate system respectively. The starting point for our method is a set of different views of a cylindrical surface, as well as a precomputed disparity map estimation between pair of images. The proposed variational technique is based on an energy minimization where we balance on the one hand the regularity of the cylindrical function given by the distance of the surface points to cylinder axis, and on the other hand, the distance between the projection of the surface points on the images and the expected location following the precomputed disparity map estimation between pair of images. One interesting advantage of this approach is that we regularize the 3D surface by means of a bi-dimensio al minimization problem. We show some experimental results for large stereo sequences.

3-D geometry reconstruction using a color image stereo pair and partial differential equations

[EN] In this work, we present a new model for a dense disparity estimation and the 3-D geometry reconstruction using a color image stereo pair. First, we present a brief introduction to the 3-D Geometry of a camera system. Next, we propose a new model for the disparity estimation based on an energy functional. We look for the local minima of the energy using the associate Euler-Langrage partial differential equations. This model is a generalization to color image of the model developed in, with some changes in the strategy to avoid the irrelevant local minima. We present some numerical experiences of 3-D reconstruction, using this method some real stereo pairs.

A variational approach to 3D geometry reconstruction from two or multiple views

[EN] In the last years we have developed some methods for 3D reconstruction. First we began with the problem of reconstructing a 3D scene from a stereoscopic pair of images. We developed some methods based on energy functionals which produce dense disparity maps by preserving discontinuities from image boundaries. Then we passed to the problem of reconstructing a 3D scene from multiple views (more than 2). The method for multiple view reconstruction relies on the method for stereoscopic reconstruction. For every pair of consecutive images we estimate a disparity map and then we apply a robust method that searches for good correspondences through the sequence of images. Recently we have proposed several methods for 3D surface regularization. This is a postprocessing step necessary for smoothing the final surface, which could be afected by noise or mismatch correspondences. These regularization methods are interesting because they use the information from the reconstructing process and not only from the 3D surface. We have tackled all these problems from an energy minimization approach. We investigate the associated Euler-Lagrange equation of the energy functional, and we approach the solution of the underlying partial differential equation (PDE) using a gradient descent method.

Specification, execution and verification of interaction protocols: an approach based on computational logic

Interaction protocols establish how different computational entities can interact with each other. The interaction can be finalized to the exchange of data, as in 'communication protocols', or can be oriented to achieve some result, as in 'application protocols'. Moreover, with the increasing complexity of modern distributed systems, protocols are used also to control such a complexity, and to ensure that the system as a whole evolves with certain features. However, the extensive use of protocols has raised some issues, from the language for specifying them to the several verification aspects. Computational Logic provides models, languages and tools that can be effectively adopted to address such issues: its declarative nature can be exploited for a protocol specification language, while its operational counterpart can be used to reason upon such specifications. In this thesis we propose a proof-theoretic framework, called SCIFF, together with its extensions. SCIFF is based on Abductive Logic Programming, and provides a formal specification language with a clear declarative semantics (based on abduction). The operational counterpart is given by a proof procedure, that allows to reason upon the specifications and to test the conformance of given interactions w.r.t. a defined protocol. Moreover, by suitably adapting the SCIFF Framework, we propose solutions for addressing (1) the protocol properties verification (g-SCIFF Framework), and (2) the a-priori conformance verification of peers w.r.t. the given protocol (AlLoWS Framework). We introduce also an agent based architecture, the SCIFF Agent Platform, where the same protocol specification can be used to program and to ease the implementation task of the interacting peers.

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.

People semantic description and re-identification from point cloud geometry

The automatic extraction of biometric descriptors of anonymous people is a challenging scenario in camera networks. This task is typically accomplished making use of visual information. Calibrated RGBD sensors make possible the extraction of point cloud information. We present a novel approach for people semantic description and re-identification using the individual point cloud information. The proposal combines the use of simple geometric features with point cloud features based on surface normals.