This thesis is devoted to the study of the hydrodynamic behavior of the unitary Fermi gas trapped by a highly elongated harmonic potential. Propagation of sound is one of the most exciting features exhibited by interacting many-body systems. It provides crucial information on the dynamic behavior of the system as well as on key thermodynamic quantities. The propagation of sound is particularly interesting in superfluids where two-fluid hydrodynamic theory predicts the occurrence of two different sounds: first sound, where the normal and superfluid component oscillate in phase, and second sound, where the two components oscillate with opposite phase. In the thesis, we investigate the propagation of sound waves of the unitary Fermi gas in a cylindrical geometry by solving the equations of two-fluid hydrodynamics in the `1D' scenario at finite temperature. The relevant thermodynamic functions entering the hydrodynamic equations are discussed in the superfluid and normal regimes in terms of universal scaling functions. Both the first sound and second sound solutions are calculated as a function of temperature and the role of the superfluid density is explicitly pointed out. The density fluctuations in the second sound wave are found to be large enough to be measured as a consequence of the finite thermal expansion coefficient of the gas, which is the strategy used in a recent experiment carried out at Innsbruck where second sound was detected in the unitary Fermi gas. We also provide an investigation of the temperature dependence of the collective oscillations of first sound nature exhibited by a highly elongated harmonically trapped Fermi gas at unitarity, including the region below the critical temperature for superfluidity. Differently from the lowest axial breathing mode, the hydrodynamic frequencies of the higher-nodal excitations show a temperature dependence, which is calculated starting from Landau two-fluid theory and using the available experimental knowledge of the equation of state.

Collisions with He+ are an important pathway for the destruction of complex organic molecules in the interstellar medium (ISM). We have carried out dissociative charge transfer reactions of He+ with two oxygen containing organic molecules, ubiquitous in ISM: dimethyl ether (DME, CH3OCH3 ) and methyl formate (MF, HCOOCH3). Since they have a prebiotic relevance, several models were developed to explain how these molecules are formed and destroyed in the ISM. The reactions have been investigated by using the home-built Guided-Ion Beam Mass Spectrometer (GIB-MS) apparatus. Absolute cross sections and branching ratios of the products have been measured as a function of the collision energy in the hyperthermal energy range (i.e. from about 0.1 eV to 7 eV). The presence of the molecular ion was not observed among the products for these reactions, which means that the nascent DME and MF radical cations are formed in a dissociative state. Insights on both the charge transfer processes have been obtained by investigating the nature of the non-adiabatic transitions between the reactant and product potential energy surfaces (PES). The PES has been represented by using a semi-empirical method to model the inter-molecular interactions. To explain the experimental evidence, two excited states of DME and MF radical cations have been invoked: He+ captures an electron from inner valence orbitals of both the organic molecules, having binding energies ~10 eV higher than the HOMO. An improved Landau-Zener-StÃ1⁄4ckelberg model has been developed to obtain the total integral cross-section to be compared with the experimental results. Inter-molecular interaction and electron densities of the orbitals involved in the reaction turned out to be key points to describe the dynamics of the two studied dissociative charge transfers. A very good agreement is obtained between the experimental and calculated total cross-sections at low collision energy, which is the most relevant range for the interstellar environment. These results represent a significant starting point to estimate rate constants for the total dissociation of DME and MF by collisions with He+ ions in the ISM at low temperatures.

Proteins are biological macromolecules that consist of long chains of small building blocks, called amino acids. These long sequences of amino acids are unique for each protein, define a specific three-dimensional structure that allows the protein to carry out a specific function in a living organism. In fact, they can catalyse metabolic reactions, respond to stimuli, provide structure and transportation routes within the cell [1]. In a cell proteins are ubiquitous. They can be soluble in water and have usually a globular shape; they can be arranged in fibers, give structural integrity to their host, and provide the infrastucture upon which small molecules are transported where needed; they can be embedded, partially or totally, in the membrane, a wall of a lipidic bilayer, of the cell and mediate the exchange of matter with the environment. In particular, membrane proteins are categorised into three groups: permanently attached to the membrane, integral membrane proteins have several structural elements that span the width of the membrane; peripheral membrane proteins are temporarily attached to the lipid bilayer by hydrophobic and electrostatic interactions, usually following a post-translational modification of a soluble protein; water-soluble proteins, like toxins, that upon aggregation, attack the membrane and cause the disrupture of the cell. In the last decades, the availability of structural information on proteins and their three-dimensional conformation enabled the rapid development of a computational tool, molecular dynamics (MD), that allows to explore biological processes and systems at a sub-nanometer scale. The idea behind MD is to integrate Newton’s equations of motion to describe the evolution of a protein within its biological environment. The refinement of the empirical potentials, called force fields, that defines the interactions of the system of interest and the increase in the computational resources of modern computers have enhanced scientists to investigate and characterise dynamics and functions of protein with high predictive power. This methodology is nowadays widely established as an in silico technique and can be considered a real computational microscope [2, 3]. Despite its successes, the complexity and the timescale involved in realisation of a biological process required the development of new techniques that accelerate the dynamics of the system under scrutiny and the sampling of conformations of the macromolecule [4]. Enhanced sampling methods are, therefore, essential for the study of conformational transitions, key events that trigger the function of a protein. In this thesis I will focus mainly on three membrane proteins I studied in my research that span different functions and interactions with the lipid bilayer. The presence of the membrane slows down the dynamics of an em- bedded protein with respect to the water-soluble counterpart [5]. In addition, it requires a specific treatment of the system and the biological conditions necessary to mimic the experiments as close as possible. Therefore, the first chapter will be devoted to introduce molecular dynamics as a computational technique to shed light on proteins dynamics and the undelying mechanisms of the functions they perform. I will discuss the algorithms that allow a predictive use of molecular dynamics in the presence of the membrane, and a better approximation of the experimental conditions in which biological data are gathered [6]. In addition, I will briefly describe the enhanced sampling methods used to investigate large conformational changes, and the analysis techniques used to extract meaningful information from the simulations. The rest of the thesis will describe the systems that I studied in my research work. In the second chapter I will digress on the prestin protein. Prestin is a motor protein and it is present in arrays in the cochlear outer cells in the mammalian hearing mechanism. Due to its coordinated contraction and elongation in response to external stimuli, this protein changes the shape of the cell allowing the transduction of the signal. This mechanism is mediated by a ligand, but there is no evidence of the transport of the ligand across the membrane. The non-mammalian ortholog of this protein is highly similar in the amino acid sequence, but it does not perform the same function. In fact it is a transporter that allows the exchange of chloride ions, and oxalate molecules, from the intracellular to extracellular environment, and viceversa. To investigate this difference, first I performed the simulation of two proteins, the expression of prestin in the rat and in the zebrafish species, in two conformations, inward open and outward open, for 700 ns each starting from homology models, due to the absence of experimental crystal structures. I assessed the relaxation of the four structures toward a stationary state, and the equilibrated systems were simulated under the action of an external electric field to mimic the cellular environment. with this second step I was able to determine the different paths of chloride ions in the two homologs in the binding to a conserved residue, S398 in rat and S401 in the zebrafish. Finally, each expression of the protein underwent biased simulations to explore possible pathways in the change from the inward to the outward conformation. The data are not definitive to draw a conclusion, although the elevator mechanism seems to favour the elevator-like transport, a mechanism proper of other proteins in the same family of the prestin. In the third chapter I will discuss the insertion of the recoverin protein, a peripheral membrane protein, in a membrane patch. Recoverin is a calcium sensor protein expressed in the vertebrate retina. The binding of two calcium ions triggers the extrusion of a myristoyl group, a post-translational modification of the N-terminus of the protein that adds a hydrophobic chain. This extrusion gives the protein an anchor to bind the lipidic bilayer, and this insertion leads to the formation of a complex with rhodopsin kinase. In collaboration with a master student, I simulated the recoverin in two conditions, both isolated and in the complex with a peptide from the rhodopsin kinase, to investigate its unbiased anchoring. We found that the insertion of the myristoyl is highly enhanced by the electrostatic interaction of the lipidic charged group and arginines of the surface of the protein. The same pattern were found in both setups, and the abovementioned interactions were no longer required to keep the protein in contact with the membran after the myristoyl penetrated the lipidic patch. In addition we analysed the communication networks of the systems and how it was affected by the presence the peptide. This could shed a light on how the recoverin-rhodopsin kinase complex assemblies itself. The last chapter will be devoted to the conformational changes of aquaporin type 4 upon aggregation. This membrane protein is a water channel, assembled in tetramers. In the human species it is present in two isoforms, M1and M23, named after the starting residue of the N-terminus. Studies shows that in the isoform M23, AQP4 aggregates and is more likely to form large orthogonal array of particles (OAPs) that are target for the antibody AQP4-IgG. This leads to an inflammatory disease, neuromyelitis optica [7]. Although the AQP4 has already been studied as a pharmaceutical target, there is no in silico study of the protein in the isonform M23. In order to mimic the OAPs, I created an assembly of four tetramers and simulated it for 800 ns. I analysed the influence of the N-terminus after the aggregation, and no evidence of a significant difference in the global behaviour of the protein were found. New insights are instead evident in the arrangement of the transmembrane segments of the protein. Further developments are being studied to have a better understanding of the aggregation mechanism.

La thèse est consacrée à un problème scientifique très important – l’étude de l’activité des mouvements islamistes sur l’arène internationale présentée sur l’exemple de l’Algérie. Présence d’un parti actif d’opposition a mis dans l’embrras le régime militaire algérien et a aggravé la crise socio-économique et politique. La comparaison du développement de la politique extérieure de l’Algérie aux confins des siècles et des étapes de l’accroissement du FIS montre que les phases essentielles de l’établissement du FIS ont rejoint les événements importants sur la scène politique à l’intérieur du pays et les moments clefs de l’activité internationale de l’Algérie. Ce que présente une nouvelle approche d’étude des relations internationales et de la société moderne. / This thesis research is consecrated to a very important scientific problem – study of activities of Islamists movements at the international arena presented at the example of Algeria. Existence of an active opposition party embarrassed Algerian military regime and complicated socio-economic and politic crisis. Comparison of evolution of the external politics of Algeria at the turn of XX century and of stages of the rise of the IFS shows that the main phases of the IFS evolution is congruent with the important events at the political scene inside of the country and the key moments of the international activity of Algeria. This is a new approach to the study of international relations and modern societies.

Les bactéries sont en permanence confrontées à des changements d'environnements. La régulation transcriptionnelle joue alors un rôle majeur dans l'adaptation des bactéries. En particulier, la bactérie phytopathogène D. dadantii s'est récemment adaptée à l'hôte végétal. Elle produit en particulier des pectate lyases (Pel) qui dégradent la pectine, ciment des parois végétales, et jouent un rôle majeur dans le développement de la maladie. Les gènes pelD et pelE, malgré la forte divergence dans leur expression, sont issus d'un transfert horizontal suivi d'une duplication récente. La question de l'intégration de ces gènes avec les régulations préexistantes s'est alors posée.Dans un premier temps, les mécanismes moléculaires détaillés de la régulation de pelD ont été étudiés. Il a été montré que cette régulation s'appuie sur un promoteur divergent de forte affinité pour l'ARN polymérase mais de faible efficacité pour la transcription et sur un arrangement stratégique de quatre sites de fixation de répresseur FIS et deux sites de l'activateur CRP. Tous ces éléments interagissent entre eux pour produire une régulation fine de l'expression de pelD. L'origine de la divergence régulatrice entre les paralogues pelD et pelE a par la suite été explorée. De manière surprenante, la divergence entre ces deux gènes et leur sélection s'appuie presque exclusivement sur un décalage de la position du promoteur de pelE (« TSS turnover ») qui l'a transformé en initiateur de la dégradation de la pectine. Ce mécanisme très fréquent chez les eucaryotes pluricellulaires (homme, drosophile, souris…) n'avait jamais encore été décrit chez les bactéries.A travers l'étude des promoteurs pelD et pelE de D. dadantii, de nouveaux mécanismes renforçant l'importance de la régulation transcriptionnelle dans les processus adaptatifs ont ainsi été découverts / Bacteria face frequent environmental changes. Transcriptional regulation plays a major role in the adaptation to these changes. In particular, the phytopathogen bacteria Dickeya have recently adapted to vegetal hosts. They produce Pecate lyases (Pel), among others, to degrade pectin in plant cell walls, which is necessary for disease development. The pelD and pelE genes, despite the strong divergence in their expression, originate from a horizontal gene transfer followed by a recent duplication. This raises the question of their integration into the preexisting regulatory networks.Detailed molecular mechanisms of the transcriptional regulation of pelD were studied first. It was shown that this regulation relies on a high-affinity but low transcription efficiency divergent promoter and a strategic arrangement of four FIS repressor binding sites and two CRP activator binding sites. These elements interact together to fine-tune the expression of pelD. Next, the origin of the regulatory divergence between the paralogous genes pelD and pelE was explored. Surprisingly, their divergence and selection relies mostly on a TSS turnover which happened on the pelE regulatory region and transformed pelE into an initiator of pectin degradation. This widespread phenomenon in multicellular eukaryotes (human, fly, mouse…) had not yet been seen in bacteria. To conclude, through the study of D. dadantii pelD and pelE promoters, new mechanisms highlighting the relevance of transcriptional regulation in adaptation were discovered in this work

This thesis was dedicated to decorate graphene sheets with metal and metal oxide nanostructures by RF sputtering technique. Two main objectives were focused in this thesis. 1) To decorate graphene sheets uniformly with metal and metal oxide nanostructure without agglomeration. 2) To explore different kinds of application of decorated graphene sheets with metal and metal oxide nanostructures In the first step, we presented the experimental study results about Nb2O5 deposition onto graphite nanoplatelets (GNPs) by the variation of the deposition process parameters. The structural, chemical and electronic properties of the decorated GNPs with Nb2O5 layers were studied. It was found that with deposition of Nb2O5 layers onto GNPs, tensile strain was developed into the planes of the GNPs. The induced tensile strain in and between the planes of GNPs increased with raising the amount of the Nb2O5 concentration. TEM images shows that GNPs decorated with around 5 to10 nm uniform layer of Nb2O5 at 100 W on their surface were successfully fabricated. From the XPS analysis it was confirmed that, by increasing Nb2O5 layer thickness on the GNPs surface with rising RF power values binding energy downshift in C 1s peak suggests a p-type doping of GNPs due to charge transfer at the interface as a consequence of the higher work function difference between the Nb2O5 (4.70 eV) and GNPs (4.33 eV). In the second step, the interface between the graphene sheets and Nb2O5 nanoparticles were studied. It was established that the structural defects were pronounced with increasing amounts of the Nb2O5 concentration. XPS measurement on graphene/Nb2O5 suggests p-type doping of graphene due to charge transfer at the interface as a consequence of the high work function of Nb2O5. The strong p-doping effect was also confirmed by Raman analysis where the positions of the G and 2D peaks of graphene gradually upshifted upon increasing the Nb2O5 concentration. The uniform distribution of decorated Nb2O5 nanoparticles onto graphene was confirmed from TEM analysis. The ferromagnetic behavior was observed for the undecorated graphene and decorated graphene with Nb2O5 nanoparticles. The ferromagnetic behavior of graphene was enhanced with decoration of the Nb2O5 nanoparticles. In the third step, the effect of the Mg concentration on the structural, chemical and morphological properties of the graphene was described. Well dispersed Mg nanoparticles were decorated onto graphene sheets. It was found that from the XRD results, different sizes of the crystalline Mg nanoparticles were obtained onto graphene sheets with variation of the process parameters.. Raman spectra indicated that G and 2D bands of the graphene were shifted to higher wavenumber with deposition of Mg nanoparticles. The well dispersed and small size of Mg nanoparticles in the range of (8-12 nm) onto graphene sheets was decorated by using a high powder vibration frequency. No agglomeration of the sputtered particles was observed with high powder vibration frequency. This observation was confirmed by TEM micrographs. XPS analysis revealed that the decorated Mg nanoparticles onto graphene were oxidized due to exposure to the atmosphere. The well dispersed decorated Mg nanoparticles onto graphene sheets were studied for the hydrogen absorption and desorption at two different temperatures 330 oC and 360 oC at 2 and 8 bars pressure. The hydrogen up taking capacity for the decorated graphene sheets with Mg nanoparticles was 3 wt. % in whole composite. However, the up taking hydrogen storage capacity of the only Mg nanoparticles was 6.6 wt. %. In the last step, the interaction of the graphene sheets with TiO2 nanoparticles was studied. The XRD results indicated that the lattice of the graphene sheets was distorted with increasing amount of the TiO2 concentration. The particle nature of the deposited TiO2 was confirmed by TEM examination and also the TEM analysis shows that TiO2 nanoparticles were uniformly distributed onto graphene sheets. The Raman analysis showed that the G and 2D bands of graphene were shifted to higher wavenumber with increasing TiO2 concentration onto graphene sheet confirming the p doped graphene with TiO2 nanoparticles. The XPS analysis further confirmed the p doping of graphene upon the deposition of the TiO2 nanoparticles. The binding energy downshift the C 1s core level of was observed after charge transfer from graphene to TiO2 nanoparticles due to the larger work function of TiO2 relatively to that of graphene. It was observed that decorated graphene sheets with TiO2 nanoparticles shows reasonably catalytic activity.

This thesis investigates two biological systems using atomistic modelling and molecular dynamics simulation. The work is focused on: (a) the study of the interaction between a segment of a DNA molecule and a functionalized surface; (b) the dynamical modelling of protein tau, an intrinsically disordered protein. We briefly describe here the two problems; for their detailed introduction we refer respectively to chapter DNA and chapter TAU. The interest in the study of the adsorption of DNA on functionalized surfaces is related to the considerable effort that in recent years has been devoted in developing technologies for faster and cheaper genome sequencing. In order to sequence a DNA molecule, it has to be extracted from the cell where it is stored (e.g. the blood cells). As a consequence any genomic analysis requires a purification process in order to remove from the DNA molecule proteins, lipids and any other contaminants. The extraction and purification of DNA from biological samples is hence the first step towards an efficient and cheap genome sequencing. Using the chemical and physical properties of DNA it is possible to generate an attractive interaction between this macromolecule and a properly treated surface. Once positioned on the surface, the DNA can be more easily purified. In this work we set up a detailed molecular model of DNA interacting with a surface functionalized with amino silanes. The intent is to investigate the free energy of adsorption of small DNA oligomers as a function of the pH and ionic strength of the solution. The tau protein belongs to the category of Intrinsically Disordered Proteins (IDP), which in their native state do not have an average stable structure and fluctuate between many conformations. In its physiological state, tau protein helps nucleating and stabilizing the microtubules in the axons of the neurons. On the other hand, the same tau - in a pathological aggregation - is involved in the development of the Alzheimer disease. IDPs do not have a definite 3D structure, therefore their dynamical simulation cannot start from a known list of atomistic positions, like a protein data bank file. We first introduce a procedure to find an initial dynamical state for a generic IDP, and we apply it to the tau protein. We then analyze the dynamical properties of tau, like the propensity of residues to form temporary secondary structures like beta-sheets or alpha-helices.

In this work we apply simulation techniques, namely Monte Carlo simulations and a path integral based method called Dominant Reaction Pathways (DRP) approach, in order to study aspects of dynamics and thermodynamics in three different families of peculiar proteins. These proteins are, for reasons such as the presence of an intermediate state in the folding path or topological constraints or large size, different from ideal systems, as may be considered small globular proteins that fold in a two state manner. The first treated topic is represented by the colicin immunity proteins IM9 and IM7, very similar in structure but with an apparently different folding mechanism. Our simulations suggest that the two proteins should fold with a similar folding mechanism via a populated on-pathway intermediate state. Then, two classes of pheromones that live in temperate and arctic water respectively are investigated. The two types of pheromones, despite the high structural similarity, show a different thermodynamic behavior, that could be explained, according to our results, by considering the role played by the location of CYS-CYS bonds along the chain. Finally, the conformational changes occurring in serpin proteins are studied. The serpins are very flexible, with a large size, more than 350 residues, and slow dynamics, from hours to weeks, completely beyond the possibilities of the simulation techniques to date. In this thesis we present the first all-atom simulations, obtained with the DRP approach, of the mechanism related to serpins and a complete characterization of the serpin dynamics is performed. Moreover, important implications for what concerns medical research field, in particular in drug design, are drown from this detailed analysis.

In this thesis an innovative approach to assess connectivity in a complex network was proposed. In network connectivity studies, a major problem is to estimate the links between the elements of a system in a robust and reliable way. To address this issue, a statistical method based on Pearson’s correlation coefficient was proposed. The former inherits the versatility of the latter, declined in a general applicability to any kind of system and the capability to evaluate cross–correlation of time series pairs both simultaneously and at different time lags. In addition, our method has an increased “investigation power”, allowing to estimate correlation at different time scale–resolutions. The method was tested on two very different kind of systems: the brain and a set of meteorological stations in the Trentino region. In both cases, the purpose was to reconstruct the existence of significant links between the elements of the two systems at different temporal resolutions. In the first case, the signals used to reconstruct the networks are magnetoencephalographic (MEG) recordings acquired from human subjects in resting–state. Zero–delays cross–correlations were estimated on a set of MEG time series corresponding to the regions belonging to the default mode network (DMN) to identify the structure of the fully–connected brain networks at different time scale resolutions. A great attention was devoted to test the correlation significance, estimated by means of surrogates of the original signal. The network structure is defined by means of the selection of four parameter values: the level of significance α, the efficiency η0, and two ranking parameters, R1 and R2, used to merge the results obtained from the whole dataset in a single average behav- ior. In the case of MEG signals, the functional fully–connected networks estimated at different time scale resolutions were compared to identify the best observation window at which the network dynamics can be highlighted. The resulting best time scale of observation was ∼ 30 s, in line with the results present in the scientific liter- ature. The same method was also applied to meteorological time series to possibly assess wind circulation networks in the Trentino region. Although this study is pre- liminary, the first results identify an interesting clusterization of the meteorological stations used in the analysis.

Title: Voluntarism in Sports - FIS Nordic Junior & U23 World Ski Championships Liberec 2013 Objectives: The main target of the thesis is to evaluate the area of voluntarism during the FIS Nordic Junior & U23 World Ski Championships Liberec 2013 and to suggest recommendations for working with volunteers during other future sports events in the Liberec area. Methods: The method of electronic survey and subsequent observation was chosen for the research. The sample of respondents was chosen from the team of FIS Nordic Junior & U23 World Ski Championships Liberec 2013 volunteers. Results: The research showed that the organization of the volunteer program at FIS World Junior and U23 athletes was evaluated by the volunteers very positively; however, the research revealed weaknesses in the individual items of the agenda. The improvements are focused on the recruitment part of the program, training of the volunteers and the final evaluation and rewarding of the volunteers. Based on the results of the research, the draft of recommendations and proposals, which are suitable for further work with volunteers at sporting events, was compiled. Keywords: Voluntarism, volunteer, FIS Nordic Junior & U23 World Ski Championships Liberec 2013, methods of working with volunteers.