The aim of this thesis is the study of electronic transport and mechanical properties of materials using computer simulations. In particular, we dealt with the charge transport in semiconduc- tor and metallic samples and with the peeling of a graphene layer from bulk graphite. The computational methods used to investigate the samples are (i) the Monte Carlo (MC) statis- tical method to simulate the transport of electrons in solids and (ii) the molecular dynamic (MD) approach to study the mechanical characteristics. A relevant part of this thesis is focused on carbon-based material, such as diamond and graphite, and the stable two-dimensional al- lotrope, graphene. The response of diamond and graphite to external electromagnetic pertur- bations, due to e.g. an impinging electron beam, was investigated by calculating reflection electron energy loss (REEL) spectra with MC simulations. By comparing the calculated spec- tra, obtained using different dielectric models, and in-house recorded experimental results, the most effective dielectric model better describing the plasma losses was identified. Moreover, an extension to these models to describe the anisotropic response of graphite to an external electromagnetic perturbation was developed and included in the MC approach. Owing to the central role of carbon for future electronic and technological applications, also its mechanical properties were investigated by means of MD simulations. In particular, the peeling process of a layer of graphene from a bulk of graphite was investigated. This process is exploitable for graphene production and for adhesive applications of this material. Moreover, the MC approach, employed for calculating REEL spectra, was tested and compared to other com- putational techniques based on the solution of the Ambartsumian-Chandrasekhar equations. This consistency test was realized by considering three metals (copper, silver and gold) as tar- get materials. Further studies were carried out on these materials by calculating secondary electron emission yields as a function of the electron beam energy. A remarkable good agreement with experimental data was obtained. The MC approach was also used to investigate the growth of particles in a W(CO)6 layer deposited on a SiO2 substrate upon irradiations by an electron beam in the context of the focused electron beam induced deposition technique. In particular, by applying the MC method, the radial distribution of emitted secondary electrons was calculated and then utilized as input data for further MD simulations. Moreover, the study of electron transport in an organic polymer (P3HT) was performed in order to understand how the molecular ordering affects the secondary electron emission. This aspect is of paramount importance to construct efficient organic electronic devices.

This thesis deals with the theoretical and computational modelling of materials by using a variety of ab-initio approaches to accurately predict the properties of realistic structures. A number of known and novel carbon-based materials are studied, exploiting the unique versatility of carbon to bind into several bonding configurations, with the aim of tailoring their electronic and mechanical characteristics. In this regard, the methods used to carry out electronic structure simulations depend on the system size: from the Dirac-Hartree-Fock approach to model molecular properties, to Density Functional Theory used for periodic solids, such as diamond and graphene-related materials composed by a few to some hundred of atoms, to Density Functional Tight Binding or plane Tight Binding to study nanowires or Beltrami pseudospheres, which are composed by some hundreds to a few millions atoms. The details of these methods are introduced in the chapters where they are used. The criterion used to present these concepts is to organize the chapters, with the exception of the last one, according to the increasing dimension of the systems. More in details, the first chapter uses the Dirac-Hartree-Fock approach to simulate atoms and molecules, such bromotrifluoromethane; the second chapter deals with periodic systems characterized by unit cells with a relatively small number of atoms, such as diamond and graphite; the third one discusses graphene and graphene-related materials with lower density; the fourth one present a new computational and experimental model of silicon carbide nanowires coated with silicon dioxide shell; the fifth chapter is focused on the study of sp2-hybridized carbon atoms, arranged on a Beltrami surface. The latter topic spans different research fields such as geometrical topology, physics and mechanical engineering. Finally, the last chapter is dedicated to an on going work which deals with the Non-Adiabatic Molecular Dynamics simulation of amorphous silica samples where we couple the nuclear dynamic of the system to the electronic structure.

The thesis reports the results of an experimental research on rare earth ion-doping effects on the structural, chemical, optical and near-infra-red photoluminescence properties of wide band gap oxide films. The aim of the work was to develop materials with good photoluminescence properties, which can be applied to increase the photovoltaic conversion efficiency of crystalline Si-based solar cells, through the increase of the most efficient and useful fraction of the solar spectrum which hits the cells, thanks to a photon frequency down-shifting process. Neodymium trivalent ion (Nd3+) was used as dopant of TiO2 and ZnO thin films. The films, with different Nd concentrations were grown onto quartz by RF plasma co-sputtering and annealed at different temperatures (400°-800°C). Different film architectures were investigated for their photoluminescence properties. Structural changes such as phase transformation from anatase to rutile, internal strain building and lattice distortion due to Nd3+ incorporation in titania, correlated with optical changes, were evidenced. Exciting titania and zinc oxide matrices with optimal Nd concentrations, with ultra-violet (UV) light energies equal to or above their gap values resulted in an efficient frequency down-shifting from UV to near-infra-red emission. The joint study of the vibrational, chemical and structural properties of the doped films allows the understanding of the excitation energy transfer process between the matrix to the ion, where self-trapped excitons can be involved. To conclude this study, the doped films were tested as down-shifter layers onto a Si-solar cell where they gave promising results. They were also tested for their photoactivity with methylene blue, showing their inhibitor effect on the photo-degradation of this organic dye molecule. Keywords: Co-Sputtering, rare earth doping, Neodymium, Titanium dioxide, Zinc oxide thin films, Photoluminescence

The propagation of light through an ultracold atomic gas is the main topic of the present work. The thesis consists of two parts. In Part I (Chapters 1,2,3), we give a complete description of the 1D photonic bands of a MI of two-level atoms paying attention to both band diagrams and reflectivity spectra. The role of regular periodicity of the system is addressed within a polariton formalism. The scattering on defects inside lattices of three-level atoms is also studied in view of optical detection of impurities in such structures. The light is used as a probe of systems engineered by the use of other laser beams. Part II (Chapters 4,5) is devoted to the development of a general framework for the time-dependent processing of a propagating slow Dark Polariton in a spatially inhomogeneous system. The coherently tunable atomic gas acts as a Dynamic Photonic Structure. Applications of this concept concerning wavelength conversion and reshaping of the pulse are also discussed for realistic experimental situations.

Graphitic materials, thanks to the lamellar structure and chemical stability, are of particular interest to realize barriers against the degradation of surface properties induced by water. Many studies showed that water could be a source of degradation of surface properties. To develop a method to overcome the problem related to the deterioration of the surface it is fundamental to study the water- material interaction. For this reason, in this thesis, the water-surface interaction of graphitic- materials and the use of graphitic materials as impermeable barriers against water were explored. Different experimental set up were realized to study the liquid-gas-solid interaction, such as time evolution of the sessile water drop contact angle, captive bubble contact angle and contact angle measurements in a controlled atmosphere. Moreover, a method of deposition of protective graphene-based films using a Meyer rod to apply graphene-inks onto a surface was developed. To understand the intrinsic wettability of graphitic materials a detailed study of the gas-liquid-solid interactions of graphite was conducted in a wide range of experimental conditions. The surface chemical properties and morphology were studied by X-ray photoelectron spectroscopy (XPS), profilometry and atomic force microscopy(AFM), sessile drop contact angle, captive bubble and secondary emission microscopy (SEM). The results of the gas-liquid–surface interaction study indicated that HOPG surface was sensitive to experimental conditions like airborne contamination and the presence of gases. Similarly, a detailed study of the interaction of water with PDMS surface in various experimental conditions (in the air and immersed in water) were conducted. The findings showed that when PDMS was immersed in water, its surface changed. In fact, the volume of air bubbles in contact with the surface of PDMS increased by increasing immersion time in the water. The experimental results indicated that such dynamic evolution of the air bubbles was related to the rearrangement of surface polymer chains via the migration of the polar groups. This phenomenon induced a degradation of the surface properties of PDMS when it is immersed in water. When graphene monolayer was added to PDMS surface, it acted as a barrier against water, suppressing the dynamic evolution of the bubble. We studied the protective properties also of graphene-based films deposited on lead (Pb). We observed that Pb surface degradation occurred when Pb was in contact with a drop of water. The results showed that degradation of Pb surface in contact with water happened very rapidly but graphene-based films, in particular, graphene oxides films, were able to reduce degradation of the surface significantly.

The properties of a broad range of materials are due to processes which occur at the nanoscale. Recently, an increasing interest has been devoted to nanostructured materials, in which the basic components are nanoscopic, and low-dimensional nanomaterials such as nanoparticles, nanowires and layered materials, in which one or more dimensions are confined. This thesis deals with nanostructured materials, in particular based on graphene, such as Graphene Nanofoams and Pillared Graphene Frameworks, and low dimensional nanomaterials such as SiC/SiO2 core/shell nanowires and graphene layers. The work is divided in four parts treating four different topics with the underlying theme of material modeling, the first two parts deal with mechanical properties and gas treatment applications, for which a description at the atomistic level is adequate, while the third and the forth focus on X-ray spectra and electron holography simulations for which electronic structure calculations are needed. The present thesis gives a general overview on various computational approaches that are useful in modeling novel low dimensional and nanostructured materials, using these approaches in dealing with specific systems.

The aims of this dissertation are twofold. Firstly, the study of superfluidity, presented in the first part, has more a fundational character, since we investigate some well known problems, already raised in the context of superfluid helium, in order to gain a deeper understanding, by exploiting the cleannes of dilute BECs systems, as well as analyzing the new features emerging from the unique dilute BECs properties. We study the BEC flow through weak-links, first analyzing the various regimes of transport by the current-phase relation and the Josephson plasma oscillations, and then turning to the superfluid instability, determining critical velocities and examining the dissipation dynamics in different geometries and dimensionalities. Secondly, the analysis of quantum interferometry, given in the second part, has instead a more technological character, since we propose two possible implementation of interferometric protocols in double-well traps, with application to the measurement of weak-forces, and study their sensitivity in detail, especially in relation to its possible quantum enhancement.

Although protein folding has been studied for decades many open issues still resist, and we yet lack a clear and general description of the mechanisms leading from the unfolded to the folded state. In particular, it is still under debate whether proteins fold through few well-defined pathways or trough a large multitude of independent ways. Answering these questions is made difficult by the fact that standard molecular dynamics (MD) simulations are very computationally expensive and often impracticable. Moreover, often even experimental techniques lack the necessary resolution to give a definitive answer. We will introduce and develope the Dominant Reaction Pathway (DRP), which is an approach that permits to efficiently study the thermally activated conformational dynamics of bio-molecules in atomistic detail. In particular, it can be used to characterize and portray the folding pathways of a protein once the unfolded and folded configurations are given. We firstly applied the DRP to a realistic protein studying the folding pathways of the Fip35 WW Domain, a 35 amino-acids long protein. Performing all atom simulations we were able to show that this small protein folds following only two pathways, defined by the order of formation of secondary structures. Notably, our results are compatible with ultra long MD simulations and consistent with the analysis of the experimental available data on the folding kinetics of the same system. Exploiting the efficiency of the DRP formalism, computing a folding trajectory of this protein only required about one hour on 48 CPU’s. We applied then our simulation scheme to a much more challenging task: performing an all-atom folding simulation of a 82 amino-acids long protein displaying a topological knot in its native conformation. We were able to portray the folding mechanism and to identify the essential key contacts leading to the proper formation of this knot. Interestingly, we showed that non native contacts, i.e., transient contacts formed during the folding of the protein but absent in its native state, can sensibly enhance the probability of correctly forming the knot.

The subject of this thesis is the use of BECs for atom interferometry. The standard way atom interferometry is today performed is by interrogating free falling samples of atoms. The employed samples are cold (but not condensed) to have high coherence, and dilute, not to interact significantly with each other. This technique represents nowadays an almost mature field of research in which the achievable interferometric sensitivity is bounded by the atomic shot noise. Until a few years ago the employment of BECs in such devices was strongly limited by the effect of the interactions between the condensed atoms. This obstacle is today removable exploiting interaction tuning techniques. The use of BECs would be advantageous for atom interferometry inasmuch they represents the matter analogue of the optical laser providing the maximum coherence allowed by quantum mechanics. Moreover, non-linear dynamic can be exploited in order to prepare entangled states of the system. The realization of entangled samples can lead to sub-shot noise sensitivity of the interferometers. At today very nice proof-of-principle experiments have been realized in this direction but a competitive device is still missing. This thesis work is inserted in a long term project whose goal is the realization of such a device. The basic operational idea of the project starts with the preparation of a BEC in a double well potential. By the effect of strong interactions the atomic system can be driven into an entangled state. Once the entangled state is prepared, interactions can be †switched off†and the interferometric sequence performed. This thesis begins with the description of the apparatus for the production of tunable BECs to be used in the interferometer. We chose to work with 39K atoms because this atomic species presents many convenient Feshabch resonances at easily accessible magnetic field values. The cooling of this particular atomic species presents many difficulties, both for the laser and evaporative cooling processes. For this reason, this was the last alkaline atom to be condensed. Its condensation up to now was only possible by employing sympathetic cooling with another species. In this thesis our solutions to the various cooling issues is reported. In particular we realized sub-Doppler cooling for the first time for this species and we achieved condensation via evaporation in an optical dipole trap taking advantage of a Feshbach resonance. In the last part of this work, are presented original calculations for the effects of thermal fluctuations on the coherence of a BEC in a double well, discussing the interplay between thermal fluctuations and interactions in this system. Estimations and feasibility studies regarding the double well trap to be realized are also reported.

In this work we will face the problem of the vibrational properties of glasses focusing on the origin and nature of the boson peak (BP). This feature is an universal characteristic of glasses and a fingerprint of the presence of disorder. Two samples have been chosen for this study. The first is permanently densified vitreous SiO$_2$. Permanent densification has been exploited to tune the glassy properties focusing on their evolution. The second sample is a silicon-selenium glass whose low sound velocity allows a detailed study of its dynamics by means of neutron inelastic scattering.