Luminescent Systems for Genomics and Proteomics

The present PhD project was focused on the development of new tools and methods for luminescence-based techniques. In particular, the ultimate goal was to present substantial improvements to the currently available technologies for both research and diagnostic in the fields of biology, proteomics and genomics. Different aspects and problems were investigated, requiring different strategies and approaches. The whole work was thus divided into separate chapters, each based on the study of one specific aspect of luminescence: Chemiluminescence, Fluorescence and Electrochemiluminescence. CHAPTER 1, Chemiluminescence The work on luminol-enhancer solution lead to a new luminol solution formulation with 1 order of magnitude lower detection limit for HRP. This technology was patented with Cyanagen brand and is now sold worldwide for Western Blot and ELISA applications. CHAPTER 2, Fluorescescence The work on dyed-doped silica nanoparticles is marking a new milestone in the development of nanotechnologies for biological applications. While the project is still in progress, preliminary studies on model structures are leading to very promising results. The improved brightness of these nano-sized objects, their simple synthesis and handling, their low toxicity will soon turn them, we strongly believe, into a new generation of fluorescent labels for many applications. CHAPTER 3, Electrochemiluminescence The work on electrochemiluminescence produced interesting results that can potentially turn into great improvements from an analytical point of view. Ru(bpy)3 derivatives were employed both for on-chip microarray (Chapter 3.1) and for microscopic imaging applications (Chapter 3.2). The development of these new techniques is still under investigation, but the obtained results confirm the possibility to achieve the final goal. Furthermore the development of new ECL-active species (Chapter 3.3, 3.4, 3.5) and their use in these applications can significantly improve overall performances, thus helping to spread ECL as powerful analytical tool for routinary techniques. To conclude, the results obtained are of strong value to largely increase the sensitivity of luminescence techniques, thus fulfilling the expectation we had at the beginning of this research work.

Classical limit of the Nelson model

Since the development of quantum mechanics it has been natural to analyze the connection between classical and quantum mechanical descriptions of physical systems. In particular one should expect that in some sense when quantum mechanical effects becomes negligible the system will behave like it is dictated by classical mechanics. One famous relation between classical and quantum theory is due to Ehrenfest. This result was later developed and put on firm mathematical foundations by Hepp. He proved that matrix elements of bounded functions of quantum observables between suitable coherents states (that depend on Planck's constant h) converge to classical values evolving according to the expected classical equations when h goes to zero. His results were later generalized by Ginibre and Velo to bosonic systems with infinite degrees of freedom and scattering theory. In this thesis we study the classical limit of Nelson model, that describes non relativistic particles, whose evolution is dictated by Schrödinger equation, interacting with a scalar relativistic field, whose evolution is dictated by Klein-Gordon equation, by means of a Yukawa-type potential. The classical limit is a mean field and weak coupling limit. We proved that the transition amplitude of a creation or annihilation operator, between suitable coherent states, converges in the classical limit to the solution of the system of differential equations that describes the classical evolution of the theory. The quantum evolution operator converges to the evolution operator of fluctuations around the classical solution. Transition amplitudes of normal ordered products of creation and annihilation operators between coherent states converge to suitable products of the classical solutions. Transition amplitudes of normal ordered products of creation and annihilation operators between fixed particle states converge to an average of products of classical solutions, corresponding to different initial conditions.

Quantum Correlations in Field Theory and Integrable Systems

In this thesis we will investigate some properties of one-dimensional quantum systems. From a theoretical point of view quantum models in one dimension are particularly interesting because they are strongly interacting, since particles cannot avoid each other in their motion, and you we can never ignore collisions. Yet, integrable models often generate new and non-trivial solutions, which could not be found perturbatively. In this dissertation we shall focus on two important aspects of integrable one- dimensional models: Their entanglement properties at equilibrium and their dynamical correlators after a quantum quench. The first part of the thesis will be therefore devoted to the study of the entanglement entropy in one- dimensional integrable systems, with a special focus on the XYZ spin-1/2 chain, which, in addition to being integrable, is also an interacting model. We will derive its Renyi entropies in the thermodynamic limit and its behaviour in different phases and for different values of the mass-gap will be analysed. In the second part of the thesis we will instead study the dynamics of correlators after a quantum quench , which represent a powerful tool to measure how perturbations and signals propagate through a quantum chain. The emphasis will be on the Transverse Field Ising Chain and the O(3) non-linear sigma model, which will be both studied by means of a semi-classical approach. Moreover in the last chapter we will demonstrate a general result about the dynamics of correlation functions of local observables after a quantum quench in integrable systems. In particular we will show that if there are not long-range interactions in the final Hamiltonian, then the dynamics of the model (non equal- time correlations) is described by the same statistical ensemble that describes its statical properties (equal-time correlations).

Impact of metal and metal oxide engineered nanoparticles in soil and plant systems

Nanotechnology promises huge benefits for society and capital invested in this new technology is steadily increasing, therefore there is a growing number of nanotechnology products on the market and inevitably engineered nanomaterials will be released in the atmosphere with potential risks to humans and environment. This study set out to extend the comprehension of the impact of metal (Ag, Co, Ni) and metal oxide (CeO2, Fe3O4, SnO2, TiO2) nanoparticles (NPs) on one of the most important environmental compartments potentially contaminated by NPs, the soil system, through the use of chemical and biological tools. For this purpose experiments were carried out to simulate realistic environmental conditions of wet and dry deposition of NPs, considering ecologically relevant endpoints. In detail, this thesis involved the study of three model systems and the evaluation of related issues: (i) NPs and bare soil, to assess the influence of NPs on the functions of soil microbial communities; (ii) NPs and plants, to evaluate the chronic toxicity and accumulation of NPs in edible tissues; (iii) NPs and invertebrates, to verify the effects of NPs on earthworms and the damaging of their functionality. The study highlighted that NP toxicity is generally influenced by NP core elements and the impact of NPs on organisms is specie-specific; moreover experiments conducted in media closer to real conditions showed a decrease in toxicity with respect to in vitro test or hydroponic tests. However, only a multidisciplinary approach, involving physical, chemical and biological skills, together with the use of advanced techniques, such as X-ray absorption fine structure spectroscopy, could pave the way to draw the right conclusions and accomplish a deeper comprehension of the effects of NPs on soil and soil inhabitants.

Photophysical investigation of light-harvesting systems for solar-to-fuel conversion

In recent years, an increasing attention has been given to the optimization of the performances of new supramolecular systems, as antennas for light collection. In such background, the aim of this thesis was the study of multichromophoric architectures capable of performing such basic action. A synthetic antenna should consist of a structure with large UV-Vis absorption cross-section, panchromatic absorption, fixed orientation of the components and suitable energy gradients between them, in order to funnel absorbed energy towards a specific site, through fast energy-transfer processes. Among the systems investigated in this thesis, three suitable classes of compounds can be identified: 1) transition metal-based multichromophoric arrays, as models for antenna construction, 2) free-base trans-A2B-phenylcorroles, as self-assembling systems to make effective mimics of the photosynthetic system, and 3) a natural harvester, the Photosystem I, immobilized on the photoanode of a solar-to-fuel conversion device. The discussion starts with the description of the photophysical properties of dinuclear quinonoid organometallic systems, able to fulfil some of the above mentioned absorption requirements, displaying in some cases panchromatic absorption. The investigation is extended to the efficient energy transfer processes occurring in supramolecular architectures, suitably organized around rigid organic scaffolds, such as spiro-bifluorene and triptycene. Furthermore, the photophysical characterization of three trans-A2B-phenylcorroles with different substituents on the meso-phenyl ring is introduced, revealing the tendency of such macrocycles to self-organize into dimers, by mimicking natural self-aggregates antenna systems. In the end, the photophysical analysis moved towards the natural super-complex PSI-LHCI, immobilized on the hematite surface of the photoanode of a bio-hybrid dye-sensitized solar cell. The importance of the entire work is related to the need for a deep understanding of the energy transfer mechanisms occurring in supramolecules, to gain insights and improve the strategies for governing the directionality of the energy flow in the construction of well-performing antenna systems.

Rigorous results in Spin Glasses and Monomer-Dimer systems

In this work I reported recent results in the field of Statistical Mechanics of Equilibrium, and in particular in Spin Glass models and Monomer Dimer models . We start giving the mathematical background and the general formalism for Spin (Disordered) Models with some of their applications to physical and mathematical problems. Next we move on general aspects of the theory of spin glasses, in particular to the Sherrington-Kirkpatrick model which is of fundamental interest for the work. In Chapter 3, we introduce the Multi-species Sherrington-Kirkpatrick model (MSK), we prove the existence of the thermodynamical limit and the Guerra's Bound for the quenched pressure together with a detailed analysis of the annealed and the replica symmetric regime. The result is a multidimensional generalization of the Parisi's theory. Finally we brie y illustrate the strategy of the Panchenko's proof of the lower bound. In Chapter 4 we discuss the Aizenmann-Contucci and the Ghirlanda-Guerra identities for a wide class of Spin Glass models. As an example of application, we discuss the role of these identities in the proof of the lower bound. In Chapter 5 we introduce the basic mathematical formalism of Monomer Dimer models. We introduce a Gaussian representation of the partition function that will be fundamental in the rest of the work. In Chapter 6, we introduce an interacting Monomer-Dimer model. Its exact solution is derived and a detailed study of its analytical properties and related physical quantities is performed. In Chapter 7, we introduce a quenched randomness in the Monomer Dimer model and show that, under suitable conditions the pressure is a self averaging quantity. The main result is that, if we consider randomness only in the monomer activity, the model is exactly solvable.