Parallel modeling of the electric field distribution in the brain

The term "Brain Imaging" identi�es a set of techniques to analyze the structure and/or functional behavior of the brain in normal and/or pathological situations. These techniques are largely used in the study of brain activity. In addition to clinical usage, analysis of brain activity is gaining popularity in others recent �fields, i.e. Brain Computer Interfaces (BCI) and the study of cognitive processes. In this context, usage of classical solutions (e.g. f MRI, PET-CT) could be unfeasible, due to their low temporal resolution, high cost and limited portability. For these reasons alternative low cost techniques are object of research, typically based on simple recording hardware and on intensive data elaboration process. Typical examples are ElectroEncephaloGraphy (EEG) and Electrical Impedance Tomography (EIT), where electric potential at the patient's scalp is recorded by high impedance electrodes. In EEG potentials are directly generated from neuronal activity, while in EIT by the injection of small currents at the scalp. To retrieve meaningful insights on brain activity from measurements, EIT and EEG relies on detailed knowledge of the underlying electrical properties of the body. This is obtained from numerical models of the electric �field distribution therein. The inhomogeneous and anisotropic electric properties of human tissues make accurate modeling and simulation very challenging, leading to a tradeo�ff between physical accuracy and technical feasibility, which currently severely limits the capabilities of these techniques. Moreover elaboration of data recorded requires usage of regularization techniques computationally intensive, which influences the application with heavy temporal constraints (such as BCI). This work focuses on the parallel implementation of a work-flow for EEG and EIT data processing. The resulting software is accelerated using multi-core GPUs, in order to provide solution in reasonable times and address requirements of real-time BCI systems, without over-simplifying the complexity and accuracy of the head models.

Characterization and modeling of the barrier properties in nanostructured systems

The object of the present study is the process of gas transport in nano-sized materials, i.e. systems having structural elements of the order of nanometers. The aim of this work is to advance the understanding of the gas transport mechanism in such materials, for which traditional models are not often suitable, by providing a correct interpretation of the relationship between diffusive phenomena and structural features. This result would allow the development new materials with permeation properties tailored on the specific application, especially in packaging systems. The methods used to achieve this goal were a detailed experimental characterization and different simulation methods. The experimental campaign regarded the determination of oxygen permeability and diffusivity in different sets of organic-inorganic hybrid coatings prepared via sol-gel technique. The polymeric samples coated with these hybrid layers experienced a remarkable enhancement of the barrier properties, which was explained by the strong interconnection at the nano-scale between the organic moiety and silica domains. An analogous characterization was performed on microfibrillated cellulose films, which presented remarkable barrier effect toward oxygen when it is dry, while in the presence of water the performance significantly drops. The very low value of water diffusivity at low activities is also an interesting characteristic which deals with its structural properties. Two different approaches of simulation were then considered: the diffusion of oxygen through polymer-layered silicates was modeled on a continuum scale with a CFD software, while the properties of n-alkanthiolate self assembled monolayers on gold were analyzed from a molecular point of view by means of a molecular dynamics algorithm. Modeling transport properties in layered nanocomposites, resulting from the ordered dispersion of impermeable flakes in a 2-D matrix, allowed the calculation of the enhancement of barrier effect in relation with platelets structural parameters leading to derive a new expression. On this basis, randomly distributed systems were simulated and the results were analyzed to evaluate the different contributions to the overall effect. The study of more realistic three-dimensional geometries revealed a prefect correspondence with the 2-D approximation. A completely different approach was applied to simulate the effect of temperature on the oxygen transport through self assembled monolayers; the structural information obtained from equilibrium MD simulations showed that raising the temperature, makes the monolayer less ordered and consequently less crystalline. This disorder produces a decrease in the barrier free energy and it lowers the overall resistance to oxygen diffusion, making the monolayer more permeable to small molecules.

CFD modeling of two-phase boiling flows in the slug flow regime with an interface capturing technique

The objective of this thesis was to improve the commercial CFD software Ansys Fluent to obtain a tool able to perform accurate simulations of flow boiling in the slug flow regime. The achievement of a reliable numerical framework allows a better understanding of the bubble and flow dynamics induced by the evaporation and makes possible the prediction of the wall heat transfer trends. In order to save computational time, the flow is modeled with an axisymmetrical formulation. Vapor and liquid phases are treated as incompressible and in laminar flow. By means of a single fluid approach, the flow equations are written as for a single phase flow, but discontinuities at the interface and interfacial effects need to be accounted for and discretized properly. Ansys Fluent provides a Volume Of Fluid technique to advect the interface and to map the discontinuous fluid properties throughout the flow domain. The interfacial effects are dominant in the boiling slug flow and the accuracy of their estimation is fundamental for the reliability of the solver. Self-implemented functions, developed ad-hoc, are introduced within the numerical code to compute the surface tension force and the rates of mass and energy exchange at the interface related to the evaporation. Several validation benchmarks assess the better performances of the improved software. Various adiabatic configurations are simulated in order to test the capability of the numerical framework in modeling actual flows and the comparison with experimental results is very positive. The simulation of a single evaporating bubble underlines the dominant effect on the global heat transfer rate of the local transient heat convection in the liquid after the bubble transit. The simulation of multiple evaporating bubbles flowing in sequence shows that their mutual influence can strongly enhance the heat transfer coefficient, up to twice the single phase flow value.

Modeling of Electric Hybrid Vehicles based on Innovative Energy Storage Technologies for Super Sports Cars Applications

Today, the contribution of the transportation sector on greenhouse gases is evident. The fast consumption of fossil fuels and its impact on the environment has given a strong impetus to the development of vehicles with better fuel economy. Hybrid electric vehicles fit into this context with different targets, starting from the reduction of emissions and fuel consumption, but also for performance and comfort enhancement. Vehicles exist with various missions; super sport cars usually aim to reach peak performance and to guarantee a great driving experience to the driver, but great attention must also be paid to fuel consumption. According to the vehicle mission, hybrid vehicles can differ in the powertrain configuration and the choice of the energy storage system. Lamborghini has recently invested in the development of hybrid super sport cars, due to performance and comfort reasons, with the possibility to reduce fuel consumption. This research activity has been conducted as a joint collaboration between the University of Bologna and the sportscar manufacturer, to analyze the impact of innovative energy storage solutions on the hybrid vehicle performance. Capacitors have been studied and modeled to analyze the pros and cons of such solution with respect to batteries. To this aim, a full simulation environment has been developed and validated to provide a concept design tool capable of precise results and able to foresee the longitudinal performance on regulated emission cycles and real driving conditions, with a focus on fuel consumption. In addition, the target of the research activity is to deepen the study of hybrid electric super sports cars in the concept development phase, focusing on defining the control strategies and the energy storage system’s technology that best suits the needs of the vehicles. This dissertation covers the key steps that have been carried out in the research project.

Characterization and modeling of low-frequency noise in MOSFETs

For many years, RF and analog integrated circuits have been mainly developed using bipolar and compound semiconductor technologies due to their better performance. In the last years, the advance made in CMOS technology allowed analog and RF circuits to be built with such a technology, but the use of CMOS technology in RF application instead of bipolar technology has brought more issues in terms of noise. The noise cannot be completely eliminated and will therefore ultimately limit the accuracy of measurements and set a lower limit on how small signals can be detected and processed in an electronic circuit. One kind of noise which affects MOS transistors much more than bipolar ones is the low-frequency noise. In MOSFETs, low-frequency noise is mainly of two kinds: flicker or 1/f noise and random telegraph signal noise (RTS). The objective of this thesis is to characterize and to model the low-frequency noise by studying RTS and flicker noise under both constant and switched bias conditions. The effect of different biasing schemes on both RTS and flicker noise in time and frequency domain has been investigated.

An New Energetic Approach to the Modeling of Human Joint Kinematics: Application to the Ankle

The objective of this dissertation is to develop and test a predictive model for the passive kinematics of human joints based on the energy minimization principle. To pursue this goal, the tibio-talar joint is chosen as a reference joint, for the reduced number of bones involved and its simplicity, if compared with other sinovial joints such as the knee or the wrist. Starting from the knowledge of the articular surface shapes, the spatial trajectory of passive motion is obtained as the envelop of joint configurations that maximize the surfaces congruence. An increase in joint congruence corresponds to an improved capability of distributing an applied load, allowing the joint to attain a better strength with less material. Thus, joint congruence maximization is a simple geometric way to capture the idea of joint energy minimization. The results obtained are validated against in vitro measured trajectories. Preliminary comparison provide strong support for the predictions of the theoretical model.

Kinematics of the Sicily and Calabria Subduction System from Elastic Block Modeling of GPS Data

We use data from about 700 GPS stations in the EuroMediterranen region to investigate the present-day behavior of the the Calabrian subduction zone within the Mediterranean-scale plates kinematics and to perform local scale studies about the strain accumulation on active structures. We focus attenction on the Messina Straits and Crati Valley faults where GPS data show extentional velocity gradients of ∼3 mm/yr and ∼2 mm/yr, respectively. We use dislocation model and a non-linear constrained optimization algorithm to invert for fault geometric parameters and slip-rates and evaluate the associated uncertainties adopting a bootstrap approach. Our analysis suggest the presence of two partially locked normal faults. To investigate the impact of elastic strain contributes from other nearby active faults onto the observed velocity gradient we use a block modeling approach. Our models show that the inferred slip-rates on the two analyzed structures are strongly impacted by the assumed locking width of the Calabrian subduction thrust. In order to frame the observed local deformation features within the present- day central Mediterranean kinematics we realyze a statistical analysis testing the indipendent motion (w.r.t. the African and Eurasias plates) of the Adriatic, Cal- abrian and Sicilian blocks. Our preferred model confirms a microplate like behaviour for all the investigated blocks. Within these kinematic boundary conditions we fur- ther investigate the Calabrian Slab interface geometry using a combined approach of block modeling and χ2ν statistic. Almost no information is obtained using only the horizontal GPS velocities that prove to be a not sufficient dataset for a multi-parametric inversion approach. Trying to stronger constrain the slab geometry we estimate the predicted vertical velocities performing suites of forward models of elastic dislocations varying the fault locking depth. Comparison with the observed field suggest a maximum resolved locking depth of 25 km.

Detection and Modeling of Boundary Layer Height

This thesis tackles the problem of the automated detection of the atmospheric boundary layer (BL) height, h, from aerosol lidar/ceilometer observations. A new method, the Bayesian Selective Method (BSM), is presented. It implements a Bayesian statistical inference procedure which combines in an statistically optimal way different sources of information. Firstly atmospheric stratification boundaries are located from discontinuities in the ceilometer back-scattered signal. The BSM then identifies the discontinuity edge that has the highest probability to effectively mark the BL height. Information from the contemporaneus physical boundary layer model simulations and a climatological dataset of BL height evolution are combined in the assimilation framework to assist this choice. The BSM algorithm has been tested for four months of continuous ceilometer measurements collected during the BASE:ALFA project and is shown to realistically diagnose the BL depth evolution in many different weather conditions. Then the BASE:ALFA dataset is used to investigate the boundary layer structure in stable conditions. Functions from the Obukhov similarity theory are used as regression curves to fit observed velocity and temperature profiles in the lower half of the stable boundary layer. Surface fluxes of heat and momentum are best-fitting parameters in this exercise and are compared with what measured by a sonic anemometer. The comparison shows remarkable discrepancies, more evident in cases for which the bulk Richardson number turns out to be quite large. This analysis supports earlier results, that surface turbulent fluxes are not the appropriate scaling parameters for profiles of mean quantities in very stable conditions. One of the practical consequences is that boundary layer height diagnostic formulations which mainly rely on surface fluxes are in disagreement to what obtained by inspecting co-located radiosounding profiles.

Structure-Property Relationships and Charge Transport Modeling of Organic Molecular Materials

From the perspective of a new-generation opto-electronic technology based on organic semiconductors, a major objective is to achieve a deep and detailed knowledge of the structure-property relationships, in order to optimize the electronic, optical, and charge transport properties by tuning the chemical-physical characteristics of the compounds. The purpose of this dissertation is to contribute to such understanding, through suitable theoretical and computational studies. Precisely, the structural, electronic, optical, and charge transport characteristics of several promising organic materials recently synthesized are investigated by means of an integrated approach encompassing quantum-chemical calculations, molecular dynamics and kinetic Monte Carlo simulations. Particular care is addressed to the rationalization of optical and charge transport properties in terms of both intra- and intermolecular features. Moreover, a considerable part of this project involves the development of a home-made set of procedures and parts of software code required to assist the modeling of charge transport properties in the framework of the non-adiabatic hopping mechanism applied to organic crystalline materials. As a first part of my investigations, I mainly discuss the optical, electronic, and structural properties of several core-extended rylene derivatives, which can be regarded to as model compounds for graphene nanoribbons. Two families have been studied, consisting in bay-linked perylene bisimide oligomers and N-annulated rylenes. Beside rylene derivatives, my studies also concerned electronic and spectroscopic properties of tetracene diimides, quinoidal oligothiophenes, and oxygen doped picene. As an example of device application, I studied the structural characteristics governing the efficiency of resistive molecular memories based on a derivative of benzoquinone. Finally, as a second part of my investigations, I concentrate on the charge transport properties of perylene bisimides derivatives. Precisely, a comprehensive study of the structural and thermal effects on the charge transport of several core-twisted chlorinated and fluoro-alkylated perylene bisimide n-type semiconductors is presented.

Experimental analysis and FE Modeling of Aluminium alloys Microstructural Evolution in Extrusion

Extrusion is a process used to form long products of constant cross section, from simple billets, with a high variety of shapes. Aluminum alloys are the materials most processed in the extrusion industry due to their deformability and the wide field of applications that range from buildings to aerospace and from design to automotive industries. The diverse applications imply different requirements that can be fulfilled by the wide range of alloys and treatments, that is from critical structural application to high quality surface and aesthetical aspect. Whether one or the other is the critical aspect, they both depend directly from microstructure. The extrusion process is moreover marked by high deformations and complex strain gradients making difficult the control of microstructure evolution that is at present not yet fully achieved. Nevertheless the evolution of Finite Element modeling has reached a maturity and can therefore start to be used as a tool for investigation and prediction of microstructure evolution. This thesis will analyze and model the evolution of microstructure throughout the entire extrusion process for 6XXX series aluminum alloys. Core phase of the work was the development of specific tests to investigate the microstructure evolution and validate the model implemented in a commercial FE code. Along with it two essential activities were carried out for a correct calibration of the model beyond the simple research of contour parameters, thus leading to the understanding and control of both code and process. In this direction activities were also conducted on building critical knowhow on the interpretation of microstructure and extrusion phenomena. It is believed, in fact, that the sole analysis of the microstructure evolution regardless of its relevance in the technological aspects of the process would be of little use for the industry as well as ineffective for the interpretation of the results.

Statistical Physics and Modeling of Human Mobility

In this thesis, we extend some ideas of statistical physics to describe the properties of human mobility. By using a database containing GPS measures of individual paths (position, velocity and covered space at a spatial scale of 2 Km or a time scale of 30 sec), which includes the 2% of the private vehicles in Italy, we succeed in determining some statistical empirical laws pointing out "universal" characteristics of human mobility. Developing simple stochastic models suggesting possible explanations of the empirical observations, we are able to indicate what are the key quantities and cognitive features that are ruling individuals' mobility. To understand the features of individual dynamics, we have studied different aspects of urban mobility from a physical point of view. We discuss the implications of the Benford's law emerging from the distribution of times elapsed between successive trips. We observe how the daily travel-time budget is related with many aspects of the urban environment, and describe how the daily mobility budget is then spent. We link the scaling properties of individual mobility networks to the inhomogeneous average durations of the activities that are performed, and those of the networks describing people's common use of space with the fractional dimension of the urban territory. We study entropy measures of individual mobility patterns, showing that they carry almost the same information of the related mobility networks, but are also influenced by a hierarchy among the activities performed. We discover that Wardrop's principles are violated as drivers have only incomplete information on traffic state and therefore rely on knowledge on the average travel-times. We propose an assimilation model to solve the intrinsic scattering of GPS data on the street network, permitting the real-time reconstruction of traffic state at a urban scale.

Computational Modeling of Cardiac Excitation-Contraction Coupling in Physiological and Pathological Conditions

The cardiomyocyte is a complex biological system where many mechanisms interact non-linearly to regulate the coupling between electrical excitation and mechanical contraction. For this reason, the development of mathematical models is fundamental in the field of cardiac electrophysiology, where the use of computational tools has become complementary to the classical experimentation. My doctoral research has been focusing on the development of such models for investigating the regulation of ventricular excitation-contraction coupling at the single cell level. In particular, the following researches are presented in this thesis: 1) Study of the unexpected deleterious effect of a Na channel blocker on a long QT syndrome type 3 patient. Experimental results were used to tune a Na current model that recapitulates the effect of the mutation and the treatment, in order to investigate how these influence the human action potential. Our research suggested that the analysis of the clinical phenotype is not sufficient for recommending drugs to patients carrying mutations with undefined electrophysiological properties. 2) Development of a model of L-type Ca channel inactivation in rabbit myocytes to faithfully reproduce the relative roles of voltage- and Ca-dependent inactivation. The model was applied to the analysis of Ca current inactivation kinetics during normal and abnormal repolarization, and predicts arrhythmogenic activity when inhibiting Ca-dependent inactivation, which is the predominant mechanism in physiological conditions. 3) Analysis of the arrhythmogenic consequences of the crosstalk between β-adrenergic and Ca-calmodulin dependent protein kinase signaling pathways. The descriptions of the two regulatory mechanisms, both enhanced in heart failure, were integrated into a novel murine action potential model to investigate how they concur to the development of cardiac arrhythmias. These studies show how mathematical modeling is suitable to provide new insights into the mechanisms underlying cardiac excitation-contraction coupling and arrhythmogenesis.

Numerical modeling of the Alto Tiberina low angle normal fault

The aim of this Thesis is to obtain a better understanding of the mechanical behavior of the active Alto Tiberina normal fault (ATF). Integrating geological, geodetic and seismological data, we perform 2D and 3D quasi-static and dynamic mechanical models to simulate the interseismic phase and rupture dynamic of the ATF. Effects of ATF locking depth, synthetic and antithetic fault activity, lithology and realistic fault geometries are taken in account. The 2D and 3D quasi-static model results suggest that the deformation pattern inferred by GPS data is consistent with a very compliant ATF zone (from 5 to 15 km) and Gubbio fault activity. The presence of the ATF compliant zone is a first order condition to redistribute the stress in the Umbria-Marche region; the stress bipartition between hanging wall (high values) and footwall (low values) inferred by the ATF zone activity could explain the microseismicity rates that are higher in the hanging wall respect to the footwall. The interseismic stress build-up is mainly located along the Gubbio fault zone and near ATF patches with higher dip (30°of 3D rupture dynamic models demonstrate that the magnitude expected, after that an event is simulated on the ATF, can decrease if we consider the fault plane roughness.

Analysis and mathematical modeling of wave-structure interaction

The aim of this thesis, included within the THESEUS project, is the development of a mathematical model 2DV two-phase, based on the existing code IH-2VOF developed by the University of Cantabria, able to represent together the overtopping phenomenon and the sediment transport. Several numerical simulations were carried out in order to analyze the flow characteristics on a dike crest. The results show that the seaward/landward slope does not affect the evolution of the flow depth and velocity over the dike crest whereas the most important parameter is the relative submergence. Wave heights decrease and flow velocities increase while waves travel over the crest. In particular, by increasing the submergence, the wave height decay and the increase of the velocity are less marked. Besides, an appropriate curve able to fit the variation of the wave height/velocity over the dike crest were found. Both for the wave height and for the wave velocity different fitting coefficients were determined on the basis of the submergence and of the significant wave height. An equation describing the trend of the dimensionless coefficient c_h for the wave height was derived. These conclusions could be taken into consideration for the design criteria and the upgrade of the structures. In the second part of the thesis, new equations for the representation of the sediment transport in the IH-2VOF model were introduced in order to represent beach erosion while waves run-up and overtop the sea banks during storms. The new model allows to calculate sediment fluxes in the water column together with the sediment concentration. Moreover it is possible to model the bed profile evolution. Different tests were performed under low-intensity regular waves with an homogeneous layer of sand on the bottom of a channel in order to analyze the erosion-deposition patterns and verify the model results.

Kinematics of local and high-z galaxies through 3D modeling of emission-line datacubes

The kinematics is a fundamental tool to infer the dynamical structure of galaxies and to understand their formation and evolution. Spectroscopic observations of gas emission lines are often used to derive rotation curves and velocity dispersions. It is however difficult to disentangle these two quantities in low spatial-resolution data because of beam smearing. In this thesis, we present 3D-Barolo, a new software to derive the gas kinematics of disk galaxies from emission-line data-cubes. The code builds tilted-ring models in the 3D observational space and compares them with the actual data-cubes. 3D-Barolo works with data at a wide range of spatial resolutions without being affected by instrumental biases. We use 3D-Barolo to derive rotation curves and velocity dispersions of several galaxies in both the local and the high-redshift Universe. We run our code on HI observations of nearby galaxies and we compare our results with 2D traditional approaches. We show that a 3D approach to the derivation of the gas kinematics has to be preferred to a 2D approach whenever a galaxy is resolved with less than about 20 elements across the disk. We moreover analyze a sample of galaxies at z~1, observed in the H-alpha line with the KMOS/VLT spectrograph. Our 3D modeling reveals that the kinematics of these high-z systems is comparable to that of local disk galaxies, with steeply-rising rotation curves followed by a flat part and H-alpha velocity dispersions of 15-40 km/s over the whole disks. This evidence suggests that disk galaxies were already fully settled about 7-8 billion years ago. In summary, 3D-Barolo is a powerful and robust tool to separate physical and instrumental effects and to derive a reliable kinematics. The analysis of large samples of galaxies at different redshifts with 3D-Barolo will provide new insights on how galaxies assemble and evolve throughout cosmic time.