Biomimetic Materials for Biomedical Applications

Objects with complex shape and functions have always attracted attention and interest. The morphological diversity and complexity of naturally occurring forms and patterns have been a motivation for humans to copy and adopt ideas from Nature to achieve functional, aesthetic and social value. Biomimetics is addressed to the design and development of new synthetic materials using strategies adopted by living organisms to produce biological materials. In particular, biomineralized tissues are often sophisticate composite materials, in which the components and the interfaces between them have been defined and optimized, and that present unusual and optimal chemical-physical, morphological and mechanical properties. Moreover, biominerals are generally produced by easily traceable raw materials, in aqueous media and at room pressure and temperature, that is through cheap process and materials. Thus, it is not surprising that the idea to mimic those strategies proper of Nature has been employed in several areas of applied sciences, such as for the preparation of liquid crystals, ceramic thin films computer switches and many other advanced materials. On this basis, this PhD thesis is focused on the investigation of the interaction of biologically active ions and molecules with calcium phosphates with the aim to develop new materials for the substitution and repair of skeletal tissue, according to the following lines: I. Modified calcium phosphates. A relevant part of this PhD thesis has been addressed to study the interaction of Strontium with calcium phosphates. It was demonstrated that strontium ion can substitute for calcium into hydroxyapatite, causing appreciable structural and morphological modifications. The detailed structural analysis carried out on the nanocrystals at different strontium content provided new insight into its interaction with the structure of hydroxyapatite. At variance with the behaviour of Sr towards HA, it was found that this ion inhibits the synthesis of octacalcium phosphate. However, it can substitute for calcium in this structure up to 15 atom %, in agreement with the increase of the cell parameters observed on increasing ion concentration. A similar behaviour was found for Magnesium ion, whereas Manganese inhibits the synthesis of octacalcium phosphate and it promotes the precipitation of dicalcium phosphate dehydrate. It was also found that Strontium affects the kinetics of the reaction of hydrolysis of α-TCP. It inhibits the conversion from α-TCP to hydroxyapatite. However, the resulting apatitic phase contains significant amounts of Sr2+ suggesting that the addition of Sr2+ to the composition of α-TCP bone cements could be successfully exploited for its local delivery in bone defects. The hydrolysis of α-TCP has been investigated also in the presence of increasing amounts of gelatin: the results indicated that this biopolymer accelerates the hydrolysis reaction and promotes the conversion of α-TCP into OCP, suggesting that its addition in the composition of calcium phosphate cements can be employed to modulate the OCP/HA ratio, and as a consequence the solubility, of the set cement. II. Deposition of modified calcium phosphates on metallic substrates. Coating with a thin film of calcium phosphates is frequently applied on the surface of metallic implants in order to combine the high mechanical strength of the metal with the excellent bioactivity of the calcium phosphates surface layers. During this PhD thesis, thank to the collaboration with prof. I.N. Mihailescu, head of the Laser-Surface-Plasma Interactions Laboratory (National Institute for Lasers, Plasma and Radiation Physics – Laser Department, Bucharest) Pulsed Laser Deposition has been successfully applied to deposit thin films of Sr substituted HA on Titanium substrates. The synthesized coatings displayed a uniform Sr distribution, a granular surface and a good degree of crystallinity which slightly decreased on increasing Sr content. The results of in vitro tests carried out on osteoblast-like and osteoclast cells suggested that the presence of Sr in HA thin films can enhance the positive effect of HA coatings on osteointegration and bone regeneration, and prevent undesirable bone resorption. The possibility to introduce an active molecule in the implant site was explored using Matrix Assisted Pulsed Laser Evaporation to deposit hydroxyapatite nanocrystals at different content of alendronate, a bisphosphonate widely employed in the treatments of pathological diseases associated to bone loss. The coatings displayed a good degree of crystallinity, and the results of in vitro tests indicated that alendronate promotes proliferation and differentiation of osteoblasts even when incorporated into hydroxyapatite. III. Synthesis of drug carriers with a delayed release modulated by a calcium phosphate coating. A core-shell system for modulated drug delivery and release has been developed through optimization of the experimental conditions to cover gelatin microspheres with a uniform layer of calcium phosphate. The kinetics of the release from uncoated and coated microspheres was investigated using aspirin as a model drug. It was shown that the presence of the calcium phosphate shell delays the release of aspirin and allows to modulate its action.

Modelling, diagnostics and experimental analysis of plasma assisted processes for material treatment

This work presents results from experimental investigations of several different atmospheric pressure plasmas applications, such as Metal Inert Gas (MIG) welding and Plasma Arc Cutting (PAC) and Welding (PAW) sources, as well as Inductively Coupled Plasma (ICP) torches. The main diagnostic tool that has been used is High Speed Imaging (HSI), often assisted by Schlieren imaging to analyse non-visible phenomena. Furthermore, starting from thermo-fluid-dynamic models developed by the University of Bologna group, such plasma processes have been studied also with new advanced models, focusing for instance on the interaction between a melting metal wire and a plasma, or considering non-equilibrium phenomena for diagnostics of plasma arcs. Additionally, the experimental diagnostic tools that have been developed for industrial thermal plasmas have been used also for the characterization of innovative low temperature atmospheric pressure non equilibrium plasmas, such as dielectric barrier discharges (DBD) and Plasma Jets. These sources are controlled by few kV voltage pulses with pulse rise time of few nanoseconds to avoid the formation of a plasma arc, with interesting applications in surface functionalization of thermosensitive materials. In order to investigate also bio-medical applications of thermal plasma, a self-developed quenching device has been connected to an ICP torch. Such device has allowed inactivation of several kinds of bacteria spread on petri dishes, by keeping the substrate temperature lower than 40 degrees, which is a strict requirement in order to allow the treatment of living tissues.

New materials for electrochemiluminescence

The study of electrochemiluminescence (ECL) involves photophysical and electrochemical aspects. Excited states are populated by an electrical stimulus. The most important applications are in the diagnostic field where a number of different biologically-relevant molecules (e.g. proteins and nucleic acids) can be recognized and quantified with a sensitivity and specificity previously not reachable. As a matter of fact the electrochemistry, differently to the classic techniques as fluorescence and chemiluminescence, allows to control the excited state generation spatially and temporally. The two research visits into A. J. Bard electrochemistry laboratories were priceless. Dr. Bard has been one of ECL pioneers, the first to introduce the technique and the one who discovered in 1972 the surprising emission of Ru(bpy)3 2+. I consider necessary to thank by now my supervisors Massimo and Francesco for their help and for giving me the great opportunity to know this unique science man that made me feel enthusiastic. I will never be grateful enough… Considering that the experimental techniques of ECL did not changed significantly in these last years the most convenient research direction has been the developing of materials with new or improved properties. In Chapter I the basics concepts and mechanisms of ECL are introduced so that the successive experiments can be easily understood. In the final paragraph the scopes of the thesis are briefly described. In Chapter II by starting from ECL experimental apparatus of Dr. Bard’s laboratories the design, assembly and preliminary tests of the new Bologna instrument are carefully described. The instrument assembly required to work hard but resulted in the introduction of the new technique in our labs by allowing the continuation of the ECL studies began in Texas. In Chapter III are described the results of electrochemical and ECL studies performed on new synthesized Ru(II) complexes containing tetrazolate based ligands. ECL emission has been investigated in solution and in solid thin films. The effect of the chemical protonation of the tetrazolate ring on ECL emission has been also investigated evidencing the possibility of a catalytic effect (generation of molecular hydrogen) of one of the complexes in organic media. Finally, after a series of preliminary studies on ECL emission in acqueous buffers, the direct interaction with calf thymus DNA of some complexes has been tested by ECL and photoluminescence (PL) titration. In Chapter IV different Ir(III) complexes have been characterized electrochemically and photophysically (ECL and PL). Some complexes were already well-known in literature for their high quantum efficiency whereas the remaining were new synthesized compounds containing tetrazolate based ligands analogous to those investigated in Chapt. III. During the tests on a halogenated complex was unexpectedly evidenced the possibility to follow the kinetics of an electro-induced chemical reaction by using ECL signal. In the last chapter (V) the possibility to use mono-use silicon chips electrodes as ECL analitycal devices is under investigation. The chapter begins by describing the chip structure and materials then a signal reproducibility study and geometry optimization is carried on by using two different complexes. In the following paragraphs is reported in detail the synthesis of an ECL label based on Ru(bpy)3 2+ and the chip functionalization by using a lipoic acid SAM and the same label. After some preliminary characterizations (mass spectroscopy TOF) has been demonstrated that by mean of a simple and fast ECL measurement it’s possible to confirm the presence of the coupling product SAM-label into the chip with a very high sensitivity. No signal was detected from the same system by using photoluminescence.

Application of FTIR microscopy to cultural heritage materials

Research in art conservation has been developed from the early 1950s, giving a significant contribution to the conservation-restoration of cultural heritage artefacts. In fact, only through a profound knowledge about the nature and conditions of constituent materials, suitable decisions on the conservation and restoration measures can thus be adopted and preservation practices enhanced. The study of ancient artworks is particularly challenging as they can be considered as heterogeneous and multilayered systems where numerous interactions between the different components as well as degradation and ageing phenomena take place. However, difficulties to physically separate the different layers due to their thickness (1-200 µm) can result in the inaccurate attribution of the identified compounds to a specific layer. Therefore, details can only be analysed when the sample preparation method leaves the layer structure intact, as for example the preparation of embedding cross sections in synthetic resins. Hence, spatially resolved analytical techniques are required not only to exactly characterize the nature of the compounds but also to obtain precise chemical and physical information about ongoing changes. This thesis focuses on the application of FTIR microspectroscopic techniques for cultural heritage materials. The first section is aimed at introducing the use of FTIR microscopy in conservation science with a particular attention to the sampling criteria and sample preparation methods. The second section is aimed at evaluating and validating the use of different FTIR microscopic analytical methods applied to the study of different art conservation issues which may be encountered dealing with cultural heritage artefacts: the characterisation of the artistic execution technique (chapter II-1), the studies on degradation phenomena (chapter II-2) and finally the evaluation of protective treatments (chapter II-3). The third and last section is divided into three chapters which underline recent developments in FTIR spectroscopy for the characterisation of paint cross sections and in particular thin organic layers: a newly developed preparation method with embedding systems in infrared transparent salts (chapter III-1), the new opportunities offered by macro-ATR imaging spectroscopy (chapter III-2) and the possibilities achieved with the different FTIR microspectroscopic techniques nowadays available (chapter III-3). In chapter II-1, FTIR microspectroscopy as molecular analysis, is presented in an integrated approach with other analytical techniques. The proposed sequence is optimized in function of the limited quantity of sample available and this methodology permits to identify the painting materials and characterise the adopted execution technique and state of conservation. Chapter II-2 describes the characterisation of the degradation products with FTIR microscopy since the investigation on the ageing processes encountered in old artefacts represents one of the most important issues in conservation research. Metal carboxylates resulting from the interaction between pigments and binding media are characterized using synthesised metal palmitates and their production is detected on copper-, zinc-, manganese- and lead- (associated with lead carbonate) based pigments dispersed either in oil or egg tempera. Moreover, significant effects seem to be obtained with iron and cobalt (acceleration of the triglycerides hydrolysis). For the first time on sienna and umber paints, manganese carboxylates are also observed. Finally in chapter II-3, FTIR microscopy is combined with further elemental analyses to characterise and estimate the performances and stability of newly developed treatments, which should better fit conservation-restoration problems. In the second part, in chapter III-1, an innovative embedding system in potassium bromide is reported focusing on the characterisation and localisation of organic substances in cross sections. Not only the identification but also the distribution of proteinaceous, lipidic or resinaceous materials, are evidenced directly on different paint cross sections, especially in thin layers of the order of 10 µm. Chapter III-2 describes the use of a conventional diamond ATR accessory coupled with a focal plane array to obtain chemical images of multi-layered paint cross sections. A rapid and simple identification of the different compounds is achieved without the use of any infrared microscope objectives. Finally, the latest FTIR techniques available are highlighted in chapter III-3 in a comparative study for the characterisation of paint cross sections. Results in terms of spatial resolution, data quality and chemical information obtained are presented and in particular, a new FTIR microscope equipped with a linear array detector, which permits reducing the spatial resolution limit to approximately 5 µm, provides very promising results and may represent a good alternative to either mapping or imaging systems.

Numerical and analytical vibro-acoustic modelling of porous materials: the Cell Method for poroelasticity and the case of inclusions

Porous materials are widely used in many fields of industrial applications, to achieve the requirements of noise reduction, that nowadays derive from strict regulations. The modeling of porous materials is still a problematic issue. Numerical simulations are often problematic in case of real complex geometries, especially in terms of computational times and convergence. At the same time, analytical models, even if partly limited by restrictive simplificative hypotheses, represent a powerful instrument to capture quickly the physics of the problem and general trends. In this context, a recently developed numerical method, called the Cell Method, is described, is presented in the case of the Biot's theory and applied for representative cases. The peculiarity of the Cell Method is that it allows for a direct algebraic and geometrical discretization of the field equations, without any reduction to a weak integral form. Then, the second part of the thesis presents the case of interaction between two poroelastic materials under the context of double porosity. The idea of using periodically repeated inclusions of a second porous material into a layer composed by an original material is described. In particular, the problem is addressed considering the efficiency of the analytical method. A analytical procedure for the simulation of heterogeneous layers based is described and validated considering both conditions of absorption and transmission; a comparison with the available numerical methods is performed. ---------------- I materiali porosi sono ampiamente utilizzati per diverse applicazioni industriali, al fine di raggiungere gli obiettivi di riduzione del rumore, che sono resi impegnativi da norme al giorno d'oggi sempre più stringenti. La modellazione dei materiali porori per applicazioni vibro-acustiche rapprensenta un aspetto di una certa complessità. Le simulazioni numeriche sono spesso problematiche quando siano coinvolte geometrie di pezzi reali, in particolare riguardo i tempi computazionali e la convergenza. Allo stesso tempo, i modelli analitici, anche se parzialmente limitati a causa di ipotesi semplificative che ne restringono l'ambito di utilizzo, rappresentano uno strumento molto utile per comprendere rapidamente la fisica del problema e individuare tendenze generali. In questo contesto, un metodo numerico recentemente sviluppato, il Metodo delle Celle, viene descritto, implementato nel caso della teoria di Biot per la poroelasticità e applicato a casi rappresentativi. La peculiarità del Metodo delle Celle consiste nella discretizzazione diretta algebrica e geometrica delle equazioni di campo, senza alcuna riduzione a forme integrali deboli. Successivamente, nella seconda parte della tesi viene presentato il caso delle interazioni tra due materiali poroelastici a contatto, nel contesto dei materiali a doppia porosità. Viene descritta l'idea di utilizzare inclusioni periodicamente ripetute di un secondo materiale poroso all'interno di un layer a sua volta poroso. In particolare, il problema è studiando il metodo analitico e la sua efficienza. Una procedura analitica per il calcolo di strati eterogenei di materiale viene descritta e validata considerando sia condizioni di assorbimento, sia di trasmissione; viene effettuata una comparazione con i metodi numerici a disposizione.

Diagnostic techniques for EHD and MHD interaction

The impact of plasma technologies is growing both in the academic and in the industrial fields. Nowadays, a great interest is focused in plasma applications in aeronautics and astronautics domains. Plasma actuators based on the Magneto-Hydro-Dynamic (MHD) and Electro- Hydro-Dynamic (EHD) interactions are potentially able to suitably modify the fluid-dynamics characteristics around a flying body without utilizing moving parts. This could lead to the control of an aircraft with negligible response time, more reliability and improvements of the performance. In order to study the aforementioned interactions, a series of experiments and a wide number of diagnostic techniques have been utilized. The EHD interaction, realized by means of a Dielectric Barrier Discharge (DBD) actuator, and its impact on the boundary layer have been evaluated by means of two different experiments. In the first one a three phase multi-electrode flat panel actuator is used. Different external flow velocities (from 1 to 20m/s) and different values of the supplied voltage and frequency have been considered. Moreover a change of the phase sequence has been done to verify the influence of the electric field existing between successive phases. Measurements of the induced speed had shown the effect of the supply voltage and the frequency, and the phase order in the momentum transfer phenomenon. Gains in velocity, inside the boundary layer, of about 5m/s have been obtained. Spectroscopic measurements allowed to determine the rotational and the vibrational temperature of the plasma which lie in the range of 320 ÷ 440°K and of 3000 ÷ 3900°K respectively. A deviation from thermodynamic equilibrium had been found. The second EHD experiment is realized on a single electrode pair DBD actuator driven by nano-pulses superimposed to a DC or an AC bias. This new supply system separates the plasma formation mechanism from the acceleration action on the fluid, leading to an higher degree of the control of the process. Both the voltage and the frequency of the nano-pulses and the amplitude and the waveform of the bias have been varied during the experiment. Plasma jets and vortex behavior had been observed by means of fast Schlieren imaging. This allowed a deeper understanding of the EHD interaction process. A velocity increase in the boundary layer of about 2m/s had been measured. Thrust measurements have been performed by means of a scales and compared with experimental data reported in the literature. For similar voltage amplitudes thrust larger than those of the literature, had been observed. Surface charge measurements led to realize a modified DBD actuator able to obtain similar performances when compared with that of other experiments. However in this case a DC bias replacing the AC bias had been used. MHD interaction experiments had been carried out in a hypersonic wind tunnel in argon with a flow of Mach 6. Before the MHD experiments a thermal, fluid-dynamic and plasma characterization of the hypersonic argon plasma flow have been done. The electron temperature and the electron number density had been determined by means of emission spectroscopy and microwave absorption measurements. A deviation from thermodynamic equilibrium had been observed. The electron number density showed to be frozen at the stagnation region condition in the expansion through the nozzle. MHD experiments have been performed using two axial symmetric test bodies. Similar magnetic configurations were used. Permanent magnets inserted into the test body allowed to generate inside the plasma azimuthal currents around the conical shape of the body. These Faraday currents are responsible of the MHD body force which acts against the flow. The MHD interaction process has been observed by means of fast imaging, pressure and electrical measurements. Images showed bright rings due to the Faraday currents heating and exciting the plasma particles. Pressure measurements showed increases of the pressure in the regions where the MHD interaction is large. The pressure is 10 to 15% larger than when the MHD interaction process is silent. Finally by means of electrostatic probes mounted flush on the test body lateral surface Hall fields of about 500V/m had been measured. These results have been used for the validation of a numerical MHD code.

B-type cytochromes of the DOMON domain superfamily (Novel redox elements of plant plasma membrane)

The aim of the present study is understanding the properties of a new group of redox proteins having in common a DOMON-type domain with characteristics of cytochromes b. The superfamily of proteins containing a DOMON of this type includes a few protein families. With the aim of better characterizing this new protein family, the present work addresses both a CyDOM protein (a cytochrome b561) and a protein only comprised of DOMON(AIR12), both of plant origin. Apoplastic ascorbate can be regenerated from monodehydroascorbate by a trans-plasma membrane redox system which uses cytosolic ascorbate as a reductant and comprises a high potential cytochrome b. We identified the major plasma membrane (PM) ascorbate-reducible b-type cytochrome of bean (Phaseolus vulgaris) and soybean (Glycine max) hypocotyls as orthologs of Arabidopsis auxin-responsive gene air12. The protein, which is glycosylated and glycosylphosphatidylinositol-anchored to the external side of the PM in vivo, was expressed in Pichia pastoris in a recombinant form, lacking the glycosylphosphatidylinositol-modification signal, and purified from the culture medium. Recombinant AIR12 is a soluble protein predicted to fold into a β-sandwich domain and belonging to the DOMON superfamily. It is shown to be a b-type cytochrome with a symmetrical α-band at 561 nm, to be fully reduced by ascorbate and fully oxidized by monodehydroascorbate. Redox potentiometry suggests that AIR12 binds two high-potential hemes (Em,7 +135 and +236 mV). Phylogenetic analyses reveal that the auxin-responsive genes AIR12 constitute a new family of plasma membrane b-type cytochromes specific to flowering plants. Although AIR12 is one of the few redox proteins of the PM characterized to date, the role of AIR12 in trans-PM electron transfer would imply interaction with other partners which are still to be identified. Another part of the present project was aimed at understanding of a soybean protein comprised of a DOMON fused with a well-defined b561 cytochrome domain (CyDOM). Various bioinformatic approaches show this protein to be composed of an N-terminal DOMON followed by b561 domain. The latter contains five transmembrane helices featuring highly conserved histidines, which might bind haem groups. The CyDOM has been cloned and expressed in the yeast Pichia pastoris, and spectroscopic analyses have been accomplished on solubilized yeast membranes. CyDOM clearly reveal the properties of b-type cytochrome. The results highlight the fact that CyDOM is clearly able to lead an electron flux through the plasmamembrane. Voltage clamp experiments demonstrate that Xenopus laevis oocytes transformed with CyDOM of soybean exhibit negative electrical currents in presence of an external electron acceptor. Analogous investigations were carried out with SDR2, a CyDOM of Drosophila melanogaster which shows an electron transport capacity even higher than plant CyDOM. As quoted above, these data reinforce those obtained in plant CyDOM on the one hand, and on the other hand allow to attribute to SDR2-like proteins the properties assigned to CyDOM. Was expressed in Regenerated tobacco roots, transiently transformed with infected a with chimeral construct GFP: CyDOM (by A. rhizogenes infection) reveals a plasmamembrane localization of CyDOM both in epidermal cells of the elongation zone of roots and in root hairs. In conclusion. Although the data presented here await to be expanded and in part clarified, it is safe to say they open a new perspective about the role of this group of proteins. The biological relevance of the functional and physiological implications of DOMON redox domains seems noteworthy, and it can but increase with future advances in research. Beyond the very finding, however interesting in itself, of DOMON domains as extracellular cytochromes, the present study testifies to the fact that cytochrome proteins containing DOMON domains of the type of “CyDOM” can transfer electrons through membranes and may represent the most important redox component of the plasmamembrane as yet discovered.

Design and optimization of components and processes for plasma sources in advanced material treatments

The research activities described in the present thesis have been oriented to the design and development of components and technological processes aimed at optimizing the performance of plasma sources in advanced in material treatments. Consumables components for high definition plasma arc cutting (PAC) torches were studied and developed. Experimental activities have in particular focussed on the modifications of the emissive insert with respect to the standard electrode configuration, which comprises a press fit hafnium insert in a copper body holder, to improve its durability. Based on a deep analysis of both the scientific and patent literature, different solutions were proposed and tested. First, the behaviour of Hf cathodes when operating at high current levels (250A) in oxidizing atmosphere has been experimentally investigated optimizing, with respect to expected service life, the initial shape of the electrode emissive surface. Moreover, the microstructural modifications of the Hf insert in PAC electrodes were experimentally investigated during first cycles, in order to understand those phenomena occurring on and under the Hf emissive surface and involved in the electrode erosion process. Thereafter, the research activity focussed on producing, characterizing and testing prototypes of composite inserts, combining powders of a high thermal conductibility (Cu, Ag) and high thermionic emissivity (Hf, Zr) materials The complexity of the thermal plasma torch environment required and integrated approach also involving physical modelling. Accordingly, a detailed line-by-line method was developed to compute the net emission coefficient of Ar plasmas at temperatures ranging from 3000 K to 25000 K and pressure ranging from 50 kPa to 200 kPa, for optically thin and partially autoabsorbed plasmas. Finally, prototypal electrodes were studied and realized for a newly developed plasma source, based on the plasma needle concept and devoted to the generation of atmospheric pressure non-thermal plasmas for biomedical applications.

Development and performance assessment of a Plasma Focus electron beam generator for Intra-Operative Radiation Therapy

The Plasma Focus is a device designed to generate a plasma sheet between two coaxial electrodes by means of a high voltage difference. The plasma is then driven to collapse into a “pinch”, where thermonuclear conditions prevail. During the “pinch phase” charged particles are emitted, with two main components: an ion beam peaked forward and an electron beam directed backward. The electron beam emitted backward by Plasma Focus devices is being investigated as a radiation source for medical applications, using it to produce x-rays by interaction with appropriate targets (through bremsstrahlung and characteristic emission). A dedicated Plasma Focus device, named PFMA-3 (Plasma Focus for Medical Applications number 3), has been designed, put in operation and tested by the research groups of the Universities of Bologna and Ferrara. The very high dose rate (several gray per discharge, in less than 1 µs) is a peculiarity of this device that has to be investigated, as it might modify the relative biological effectiveness (RBE). Aim of this Ph.D. project was to investigate the main physical properties of the low-energy x-ray beams produced by a Plasma Focus device and their potential medical applications to IORT treatments. It was necessary to develop the optimal geometrical configuration; to evaluate the x-rays produced and their dose deposited; to estimate the energy electron spectrum produced in the “pinch phase”; to study an optimal target for the conversion of the x-rays; to conduct simulations to study the physics involved; and in order to evaluate the radio-biological features of the beam, cell holders had to be developed for both irradiations and cell growth conditions.

Modeling and simulations of some anisotropic soft-matter systems: from biaxial to chiral materials

We have modeled various soft-matter systems with molecular dynamics (MD) simulations. The first topic concerns liquid crystal (LC) biaxial nematic (Nb) phases, that can be possibly used in fast displays. We have investigated the phase organization of biaxial Gay-Berne (GB) mesogens, considering the effects of the orientation, strength and position of a molecular dipole. We have observed that for systems with a central dipole, nematic biaxial phases disappear when increasing dipole strength, while for systems characterized by an offset dipole, the Nb phase is stabilized at very low temperatures. In a second project, in view of their increasing importance as nanomaterials in LC phases, we are developing a DNA coarse-grained (CG) model, in which sugar and phosphate groups are represented with Lennard-Jones spheres, while bases with GB ellipsoids. We have obtained shape, position and orientation parameters for each bead, to best reproduce the atomistic structure of a B-DNA helix. Starting from atomistic simulations results, we have completed a first parametrization of the force field terms, accounting for bonded (bonds, angles and dihedrals) and non-bonded interactions (H-bond and stacking). We are currently validating the model, by investigating stability and melting temperature of various sequences. Finally, in a third project, we aim to explain the mechanism of enantiomeric discrimination due to the presence of a chiral helix of poly(gamma-benzyl L-glutamate) (PBLG), in solution of dimethylformamide (DMF), interacting with chiral or pro-chiral molecules (in our case heptyl butyrate, HEP), after tuning properly an atomistic force field (AMBER). We have observed that DMF and HEP molecules solvate uniformly the PBLG helix, but the pro-chiral solute is on average found closer to the helix with respect to the DMF. The solvent presents a faster isotropic diffusion, twice as HEP, also indicating a stronger interaction of the solute with the helix.

Soil-structure interaction during tunnelling in urban area: observations and 3D numerical modelling

This work illustrates a soil-tunnel-structure interaction study performed by an integrated,geotechnical and structural,approach based on 3D finite element analyses and validated against experimental observations.The study aims at analysing the response of reinforced concrete framed buildings on discrete foundations in interaction with metro lines.It refers to the case of the twin tunnels of the Milan (Italy) metro line 5,recently built in coarse grained materials using EPB machines,for which subsidence measurements collected along ground and building sections during tunnelling were available.Settlements measured under freefield conditions are firstly back interpreted using Gaussian empirical predictions. Then,the in situ measurements’ analysis is extended to include the evolving response of a 9 storey reinforced concrete building while being undercrossed by the metro line.In the finite element study,the soil mechanical behaviour is described using an advanced constitutive model. This latter,when combined with a proper simulation of the excavation process, proves to realistically reproduce the subsidence profiles under free field conditions and to capture the interaction phenomena occurring between the twin tunnels during the excavation. Furthermore, when the numerical model is extended to include the building, schematised in a detailed manner, the results are in good agreement with the monitoring data for different stages of the twin tunnelling. Thus, they indirectly confirm the satisfactory performance of the adopted numerical approach which also allows a direct evaluation of the structural response as an outcome of the analysis. Further analyses are also carried out modelling the building with different levels of detail. The results highlight that, in this case, the simplified approach based on the equivalent plate schematisation is inadequate to capture the real tunnelling induced displacement field. The overall behaviour of the system proves to be mainly influenced by the buried portion of the building which plays an essential role in the interaction mechanism, due to its high stiffness.

Computational insight into materials properties

The aim of the work was to explore the practical applicability of molecular dynamics at different length and time scales. From nanoparticles system over colloids and polymers to biological systems like membranes and finally living cells, a broad range of materials was considered from a theoretical standpoint. In this dissertation five chemistry-related problem are addressed by means of theoretical and computational methods. The main results can be outlined as follows. (1) A systematic study of the effect of the concentration, chain length, and charge of surfactants on fullerene aggregation is presented. The long-discussed problem of the location of C60 in micelles was addressed and fullerenes were found in the hydrophobic region of the micelles. (2) The interactions between graphene sheet of increasing size and phospholipid membrane are quantitatively investigated. (3) A model was proposed to study structure, stability, and dynamics of MoS2, a material well-known for its tribological properties. The telescopic movement of nested nanotubes and the sliding of MoS2 layers is simulated. (4) A mathematical model to gain understaning of the coupled diffusion-swelling process in poly(lactic-co-glycolic acid), PLGA, was proposed. (5) A soft matter cell model is developed to explore the interaction of living cell with artificial surfaces. The effect of the surface properties on the adhesion dynamics of cells are discussed.