Advanced applications of X-ray Absorption Spectroscopy to the study of protein metal sites.

We present a study of the metal sites of different proteins through X-ray Absorption Fine Structure (XAFS) spectroscopy. First of all, the capabilities of XAFS analysis have been improved by ab initio simulation of the near-edge region of the spectra, and an original analysis method has been proposed. The method subsequently served ad a tool to treat diverse biophysical problems, like the inhibition of proton-translocating proteins by metal ions and the matrix effect exerted on photosynthetic proteins (the bacterial Reaction Center, RC) by strongly dehydrate sugar matrices. A time-resolved study of Fe site of RC with μs resolution has been as well attempted. Finally, a further step aimed to improve the reliability of XAFS analysis has been performed by calculating the dynamical parameters of the metal binding cluster by means of DFT methods, and the theoretical result obtained for MbCO has been successfully compared with experimental data.

Numerical study of graphene as a channel material for field-effect transistors

Graphene excellent properties make it a promising candidate for building future nanoelectronic devices. Nevertheless, the absence of an energy gap is an open problem for the transistor application. In this thesis, graphene nanoribbons and pattern-hydrogenated graphene, two alternatives for inducing an energy gap in graphene, are investigated by means of numerical simulations. A tight-binding NEGF code is developed for the simulation of GNR-FETs. To speed up the simulations, the non-parabolic effective mass model and the mode-space tight-binding method are developed. The code is used for simulation studies of both conventional and tunneling FETs. The simulations show the great potential of conventional narrow GNR-FETs, but highlight at the same time the leakage problems in the off-state due to various tunneling mechanisms. The leakage problems become more severe as the width of the devices is made larger, and thus the band gap smaller, resulting in a poor on/off current ratio. The tunneling FET architecture can partially solve these problems thanks to the improved subthreshold slope; however, it is also shown that edge roughness, unless well controlled, can have a detrimental effect in the off-state performance. In the second part of this thesis, pattern-hydrogenated graphene is simulated by means of a tight-binding model. A realistic model for patterned hydrogenation, including disorder, is developed. The model is validated by direct comparison of the momentum-energy resolved density of states with the experimental angle-resolved photoemission spectroscopy. The scaling of the energy gap and the localization length on the parameters defining the pattern geometry is also presented. The results suggest that a substantial transport gap can be attainable with experimentally achievable hydrogen concentration.

The coupling between electron transfer and Protein/Solvent Dynamics in Photosynthetic Reaction Centers: Spectroscopic Studies in Amorphous Matrices

We investigated at the molecular level protein/solvent interactions and their relevance in protein function through the use of amorphous matrices at room temperature. As a model protein, we used the bacterial photosynthetic reaction center (RC) of Rhodobacter sphaeroides, a pigment protein complex which catalyzes the light-induced charge separation initiating the conversion of solar into chemical energy. The thermal fluctuations of the RC and its dielectric conformational relaxation following photoexcitation have been probed by analyzing the recombination kinetics of the primary charge-separated (P+QA-) state, using time resolved optical and EPR spectroscopies. We have shown that the RC dynamics coupled to this electron transfer process can be progressively inhibited at room temperature by decreasing the water content of RC films or of RC-trehalose glassy matrices. Extensive dehydration of the amorphous matrices inhibits RC relaxation and interconversion among conformational substates to an extent comparable to that attained at cryogenic temperatures in water-glycerol samples. An isopiestic method has been developed to finely tune the hydration level of the system. We have combined FTIR spectral analysis of the combination and association bands of residual water with differential light-minus-dark FTIR and high-field EPR spectroscopy to gain information on thermodynamics of water sorption, and on structure/dynamics of the residual water molecules, of protein residues and of RC cofactors. The following main conclusions were reached: (i) the RC dynamics is slaved to that of the hydration shell; (ii) in dehydrated trehalose glasses inhibition of protein dynamics is most likely mediated by residual water molecules simultaneously bound to protein residues and sugar molecules at the protein-matrix interface; (iii) the local environment of cofactors is not involved in the conformational dynamics which stabilizes the P+QA-; (iv) this conformational relaxation appears to be rather delocalized over several aminoacidic residues as well as water molecules weakly hydrogen-bonded to the RC.

Chemistry of aerosol particles and fog droplets during fall-winter season in the Po Valley

Air quality represents a key issue in the so-called pollution “hot spots”: environments in which anthropogenic sources are concentrated and dispersion of pollutants is limited. One of these environments, the Po Valley, normally experiences exceedances of PM10 and PM2.5 concentration limits, especially in winter when the ventilation of the lower layers of the atmosphere is reduced. This thesis provides a highlight of the chemical properties of particulate matter and fog droplets in the Po Valley during the cold season, when fog occurrence is very frequent. Fog-particles interactions were investigated with the aim to determine their impact on the regional air quality. Size-segregated aerosol samples were collected in Bologna, urban site, and San Pietro Capofiume (SPC), rural site, during two campaigns (November 2011; February 2013) in the frame of Supersito project. The comparison between particles size-distribution and chemical composition in both sites showed the relevant contribution of the regional background and secondary processes in determining the Po Valley aerosol concentration. Occurrence of fog in November 2011 campaign in SPC allowed to investigate the role of fog formation and fog chemistry in the formation, processing and deposition of PM10. Nucleation scavenging was investigated with relation to the size and the chemical composition of particles. We found that PM1 concentration is reduced up to 60% because of fog scavenging. Furthermore, aqueous-phase secondary aerosol formation mechanisms were investigated through time-resolved measurements. In SPC fog samples have been systematically collected and analysed since the nineties; a 20 years long database has been assembled. This thesis reports for the first time the results of this long time series of measurements, showing a decrease of sulphate and nitrate concentration and an increase of pH that reached values close to neutrality. A detailed discussion about the occurred changes in fog water composition over two decades is presented.