Knot theory and its applications

Nella tesi verranno presi in considerazione tre aspetti: si descriverà come la teoria dei nodi si sia sviluppata nel corso degli anni in relazione alle diverse scoperte scientifiche avvenute. Si potrà quindi subito avere una idea di come questa teoria sia estremamente connessa a diverse altre. Nel secondo capitolo ci si occuperà degli aspetti più formali di questa teoria. Si introdurrà il concetto di nodi equivalenti e di invariante dei nodi. Si definiranno diversi invarianti, dai più elementari, le mosse di Reidemeister, il numero di incroci e la tricolorabilità, fino ai polinomi invarianti, tra cui il polinomio di Alexander, il polinomio di Jones e quello di Kaufman. Infine si spiegheranno alcune applicazioni della teoria dei nodi in chimica, fisica e biologia. Sulla chimica, si definirà la chiralità molecolare e si mostrerà come la chiralità dei nodi possa essere utile nel determinare quella molecolare. In campo fisico, si mostrerà la relazione che esiste tra l'equazione di Yang-Baxter e i nodi. E in conclusione si mostrerà come modellare un importante processo biologico, la recombinazione del DNA, grazie alla teoria dei nodi.

Surface preparation and characterization of semipolar (20-21) ingan layers

In questa tesi vengono studiate le proprietà fisiche della superficie di eterostrutture InGaN/GaN cresciute con orientazione semipolare (20-21). Questi materiali fornirebbero una valida alternativa alle eterostrutture cresciute secondo la tradizionale direzione di crescita polare (0001) per la realizzazione di LED e diodi laser. I dispositivi cresciuti con orientazione semipolare (20-21) sono studiati soltanto da pochi anni e hanno già fornito dei risultati che incitano significativamente il proseguimento della ricerca in questo campo. Oltre all’ottimizzazione dell’efficienza di questi dispositivi, sono richieste ulteriori ricerche al fine di raccogliere delle informazioni mancanti come un chiaro modello strutturale della superficie (20-21). I capitoli 1 e 2 forniscono un quadro generale sul vasto campo dei semiconduttori basati sui nitruri del terzo gruppo. Il capitolo 1 tratta le proprietà generali, come le caratteristiche della struttura cristallina della wurtzite, l’energy gap e il più comune metodo di crescita epitassiale. Il capitolo 2 tratta le proprietà specifiche della superficie (20-21) come struttura, morfologia e proprietà legate all’eterostruttura InGaN/GaN (incorporazione di indio, strain e spessore critico). Nel capitolo 3 vengono descritte sinteticamente le tecniche sperimentali utilizzate per studiare i campioni di InGaN. Molte di queste tecniche richiedono condizioni operative di alto vuoto e appositi metodi di preparazione superficiale. Nel capitolo 4 vengono discussi i risultati sperimentali riguardanti la preparazione superficiale e le proprietà strutturali dei campioni. Il trattamento termico in ambiente ricco di azoto si rivela essere un metodo molto efficiente per ottenere superfici pulite. La superficie dei campioni presenta una morfologia ondulatoria e una cella unitaria superficiale di forma rettangolare. Nel capitolo 4 vengono discussi i risultati sperimentali relativi alle proprietà elettroniche e ottiche dei campioni. Immagini alla risoluzione atomica rivelano la presenza di ondulazioni alla scala dei nanometri. Vengono misurati l’energy gap e l’incurvamento superficiale della bande. Inoltre vengono identificate una serie di transizioni interbanda dovute all’interfaccia InGaN/GaN.

Fractal sets and their applications in medicine

La geometria euclidea risulta spesso inadeguata a descrivere le forme della natura. I Frattali, oggetti interrotti e irregolari, come indica il nome stesso, sono più adatti a rappresentare la forma frastagliata delle linee costiere o altri elementi naturali. Lo strumento necessario per studiare rigorosamente i frattali sono i teoremi riguardanti la misura di Hausdorff, con i quali possono definirsi gli s-sets, dove s è la dimensione di Hausdorff. Se s non è intero, l'insieme in gioco può riconoscersi come frattale e non presenta tangenti e densità in quasi nessun punto. I frattali più classici, come gli insiemi di Cantor, Koch e Sierpinski, presentano anche la proprietà di auto-similarità e la dimensione di similitudine viene a coincidere con quella di Hausdorff. Una tecnica basata sulla dimensione frattale, detta box-counting, interviene in applicazioni bio-mediche e risulta utile per studiare le placche senili di varie specie di mammiferi tra cui l'uomo o anche per distinguere un melanoma maligno da una diversa lesione della cute.

Preparation and characterization of grafted nonwoven membranes for bioseparations

Protein purification plays a crucial role in biotechnology and biomanufacturing, where downstream unit operations account for 40%-80% of the overall costs. To overcome this issue, companies strive to simplify the separation process by reducing the number of steps and replacing expensive separation devices. In this context, commercially available polybutylene terephthalate (PBT) melt-blown nonwoven membranes have been developed as a novel disposable membrane chromatography support. The PBT nonwoven membrane is able to capture products and reduce contaminants by ion exchange chromatography. The PBT nonwoven membrane was modified by grafting a poly(glycidyl methacrylate) (GMA) layer by either photo-induced graft polymerization or heat induced graft polymerization. The epoxy groups of GMA monomer were subsequently converted into cation and anion exchangers by reaction with either sulfonic acid groups or diethylamine (DEA), respectively. Several parameters of the procedure were studied, especially the effect of (i) % weight gain and (ii) ligand density on the static protein binding capacity. Bovine Serum Albumin (BSA) and human Immunoglobulin G (hIgG) were utilized as model proteins in the anion and cation exchange studies. The performance of ion exchange PBT nonwovens by HIG was evaluated under flow conditions. The anion- and cation- exchange HIG PBT nonwovens were evaluated for their ability to selectively adsorb and elute BSA or hIgG from a mixture of proteins. Cation exchange nonwovens were not able to reach a good protein separation, whereas anion exchange HIG nonwovens were able to absorb and elute BSA with very high value of purity and yield, in only one step of purification.

Preparation and assessment of immobilized laccase-based micro- and nanocatalysts for the degradation of anthropogenic compounds

Since the dawn of its presence on earth, the human being has been able to exploit the enzymes for its subsistence. More recent is the meeting between the enzymatic processes and the urgent need for technologies that aim to preserve our planet. In this field nowadays enzymatic catalysis is tested either to depollution/remediation as well as waste disposal. The work presented in this thesis, regarding both these two topics, is tailored on two European projects (EU 2020), MADFORWATER and TERMINUS respectively. Firstly, production of micro- and nanocatalysts via immobilization of laccases (a lignin-degrader enzyme) is performed. In the second part of the thesis laccase is applied to a tertiary treatment of wastewater with the aim to degrade 9 pharmaceutical active compounds in batch reactors. Despite several optimizations, poor degradation is reached and we did not proceed with the study of different bioreactor setups. Therefore, the focus is moved to a project concerning the production of smart multi-layer plastic packaging containing enzymes to improve the possibilities of recycling. In this field shielded nanocatalysts produced via coating techniques able to interact with redox mediators are investigated. The target substrate in this second project is produced in laboratory (i.e. polyurethane like compounds), starting from monomers whose degradation had already been tested, as a proof of concept. The first enzyme studied is still the laccase.

Preparation and Characterization of Polymeric Beads and Membranes for Boron Removal From Water

Boron is an element essential for various biological processes, nevertheless at high concentration it can cause health issues in both plants and animals, thus making boron a pollutant element. Low cost and effective polymeric adsorbents capable of removing boron in aqueous solution at neutral pH were prepared for this purpose. The adsorbent selectivity towards boron was conferred taking advantage of the interaction between boric acid and the alcoholic groups of N-methyl-D-Glucamine, which are able to form specific complexes. Two different kinds of devices were produced and tested: cross-linked chitosan hydrogel beads (CCBMG) and PVA/chitosan membranes, the latter taking advantage of scCO2-assisted phase inversion technique. The capability of the adsorbents to be regenerated and to allow recovery of boric acid from a solution emulating the concentration of boric acid in seawater were evaluated.

State of the art and future perspectives on security metrics and their applications

In modern society, security issues of IT Systems are intertwined with interdisciplinary aspects, from social life to sustainability, and threats endanger many aspects of every- one’s daily life. To address the problem, it’s important that the systems that we use guarantee a certain degree of security, but to achieve this, it is necessary to be able to give a measure to the amount of security. Measuring security is not an easy task, but many initiatives, including European regulations, want to make this possible. One method of measuring security is based on the use of security metrics: those are a way of assessing, from various aspects, vulnera- bilities, methods of defense, risks and impacts of successful attacks then also efficacy of reactions, giving precise results using mathematical and statistical techniques. I have done literature research to provide an overview on the meaning, the effects, the problems, the applications and the overall current situation over security metrics, with particular emphasis in giving practical examples. This thesis starts with a summary of the state of the art in the field of security met- rics and application examples to outline the gaps in current literature, the difficulties found in the change of application context, to then advance research questions aimed at fostering the discussion towards the definition of a more complete and applicable view of the subject. Finally, it stresses the lack of security metrics that consider interdisciplinary aspects, giving some potential starting point to develop security metrics that cover all as- pects involved, taking the field to a new level of formal soundness and practical usability.

Biopolyester fibers for sustainable and biocompatible applications

The rising of concerns around the scarcity of non-renewable resources has raised curiosity around new frontiers in the polymer science field. Biopolymers is a general term describing different kind of polymers that are linked with the biological world because of either monomer derivation, end of life degradation or both. The current work is aimed at studying one example of both biopolymers types. Polyhydroxibutyrate (P3HB) is a biodegradable microbial-produced polymer which holds massive potentiality as a substitute of polyolefins such as polypropylene. Though, its highly crystalline nature and stereoregularity of structure make it difficult to work with. The project P3HB-Mono take advantage of polarized Raman spectroscopy to see how annealing of chains with different weights influence the crystallinity and molecular structure of the polymer, eventually reflecting on its mechanical properties. The technique employed is also optimal in order to see how mesophase, a particular conformation of chains different from crystalline and amorphous phase, develops in the polymer structure and changes depending on temperature and mechanical stress applied to the fiber. Polycaprolactone (PCL) on the other hand is a biodegradable fossil-fuel polymer which has biocompatibility and bio-resorbability features. As a consequence this material is very appealing for medical industry and can be used for different applications in this field. One interesting option is to produce narrow and long liquid filled fibers for drug delivery inside human body, using a traditional technique in an innovative way. The project BioLiCoF investigates the feasability of producing liquid filled fibers using melt-spinning techniques and will examine the role that melt-spinning parameters and liquids employed as a core solution have on the final fiber. The physical analysis of the fibers is also interpreted and idea on future developments of the trials are suggested.

Bioremediation of PAHs - Limitations and soultions

Introduction 1.1 Occurrence of polycyclic aromatic hydrocarbons (PAH) in the environment Worldwide industrial and agricultural developments have released a large number of natural and synthetic hazardous compounds into the environment due to careless waste disposal, illegal waste dumping and accidental spills. As a result, there are numerous sites in the world that require cleanup of soils and groundwater. Polycyclic aromatic hydrocarbons (PAHs) are one of the major groups of these contaminants (Da Silva et al., 2003). PAHs constitute a diverse class of organic compounds consisting of two or more aromatic rings with various structural configurations (Prabhu and Phale, 2003). Being a derivative of benzene, PAHs are thermodynamically stable. In addition, these chemicals tend to adhere to particle surfaces, such as soils, because of their low water solubility and strong hydrophobicity, and this results in greater persistence under natural conditions. This persistence coupled with their potential carcinogenicity makes PAHs problematic environmental contaminants (Cerniglia, 1992; Sutherland, 1992). PAHs are widely found in high concentrations at many industrial sites, particularly those associated with petroleum, gas production and wood preserving industries (Wilson and Jones, 1993). 1.2 Remediation technologies Conventional techniques used for the remediation of soil polluted with organic contaminants include excavation of the contaminated soil and disposal to a landfill or capping - containment - of the contaminated areas of a site. These methods have some drawbacks. The first method simply moves the contamination elsewhere and may create significant risks in the excavation, handling and transport of hazardous material. Additionally, it is very difficult and increasingly expensive to find new landfill sites for the final disposal of the material. The cap and containment method is only an interim solution since the contamination remains on site, requiring monitoring and maintenance of the isolation barriers long into the future, with all the associated costs and potential liability. A better approach than these traditional methods is to completely destroy the pollutants, if possible, or transform them into harmless substances. Some technologies that have been used are high-temperature incineration and various types of chemical decomposition (for example, base-catalyzed dechlorination, UV oxidation). However, these methods have significant disadvantages, principally their technological complexity, high cost , and the lack of public acceptance. Bioremediation, on the contrast, is a promising option for the complete removal and destruction of contaminants. 1.3 Bioremediation of PAH contaminated soil & groundwater Bioremediation is the use of living organisms, primarily microorganisms, to degrade or detoxify hazardous wastes into harmless substances such as carbon dioxide, water and cell biomass Most PAHs are biodegradable unter natural conditions (Da Silva et al., 2003; Meysami and Baheri, 2003) and bioremediation for cleanup of PAH wastes has been extensively studied at both laboratory and commercial levels- It has been implemented at a number of contaminated sites, including the cleanup of the Exxon Valdez oil spill in Prince William Sound, Alaska in 1989, the Mega Borg spill off the Texas coast in 1990 and the Burgan Oil Field, Kuwait in 1994 (Purwaningsih, 2002). Different strategies for PAH bioremediation, such as in situ , ex situ or on site bioremediation were developed in recent years. In situ bioremediation is a technique that is applied to soil and groundwater at the site without removing the contaminated soil or groundwater, based on the provision of optimum conditions for microbiological contaminant breakdown.. Ex situ bioremediation of PAHs, on the other hand, is a technique applied to soil and groundwater which has been removed from the site via excavation (soil) or pumping (water). Hazardous contaminants are converted in controlled bioreactors into harmless compounds in an efficient manner. 1.4 Bioavailability of PAH in the subsurface Frequently, PAH contamination in the environment is occurs as contaminants that are sorbed onto soilparticles rather than in phase (NAPL, non aqueous phase liquids). It is known that the biodegradation rate of most PAHs sorbed onto soil is far lower than rates measured in solution cultures of microorganisms with pure solid pollutants (Alexander and Scow, 1989; Hamaker, 1972). It is generally believed that only that fraction of PAHs dissolved in the solution can be metabolized by microorganisms in soil. The amount of contaminant that can be readily taken up and degraded by microorganisms is defined as bioavailability (Bosma et al., 1997; Maier, 2000). Two phenomena have been suggested to cause the low bioavailability of PAHs in soil (Danielsson, 2000). The first one is strong adsorption of the contaminants to the soil constituents which then leads to very slow release rates of contaminants to the aqueous phase. Sorption is often well correlated with soil organic matter content (Means, 1980) and significantly reduces biodegradation (Manilal and Alexander, 1991). The second phenomenon is slow mass transfer of pollutants, such as pore diffusion in the soil aggregates or diffusion in the organic matter in the soil. The complex set of these physical, chemical and biological processes is schematically illustrated in Figure 1. As shown in Figure 1, biodegradation processes are taking place in the soil solution while diffusion processes occur in the narrow pores in and between soil aggregates (Danielsson, 2000). Seemingly contradictory studies can be found in the literature that indicate the rate and final extent of metabolism may be either lower or higher for sorbed PAHs by soil than those for pure PAHs (Van Loosdrecht et al., 1990). These contrasting results demonstrate that the bioavailability of organic contaminants sorbed onto soil is far from being well understood. Besides bioavailability, there are several other factors influencing the rate and extent of biodegradation of PAHs in soil including microbial population characteristics, physical and chemical properties of PAHs and environmental factors (temperature, moisture, pH, degree of contamination). Figure 1: Schematic diagram showing possible rate-limiting processes during bioremediation of hydrophobic organic contaminants in a contaminated soil-water system (not to scale) (Danielsson, 2000). 1.5 Increasing the bioavailability of PAH in soil Attempts to improve the biodegradation of PAHs in soil by increasing their bioavailability include the use of surfactants , solvents or solubility enhancers.. However, introduction of synthetic surfactant may result in the addition of one more pollutant. (Wang and Brusseau, 1993).A study conducted by Mulder et al. showed that the introduction of hydropropyl-ß-cyclodextrin (HPCD), a well-known PAH solubility enhancer, significantly increased the solubilization of PAHs although it did not improve the biodegradation rate of PAHs (Mulder et al., 1998), indicating that further research is required in order to develop a feasible and efficient remediation method. Enhancing the extent of PAHs mass transfer from the soil phase to the liquid might prove an efficient and environmentally low-risk alternative way of addressing the problem of slow PAH biodegradation in soil.

Multicelled Behaviour in E. coli: Design and experimental characterization of an engineered library of hybrid promoters.

Synthetic biology has recently had a great development, many papers have been published and many applications have been presented, spanning from the production of biopharmacheuticals to the synthesis of bioenergetic substrates or industrial catalysts. But, despite these advances, most of the applications are quite simple and don’t fully exploit the potential of this discipline. This limitation in complexity has many causes, like the incomplete characterization of some components, or the intrinsic variability of the biological systems, but one of the most important reasons is the incapability of the cell to sustain the additional metabolic burden introduced by a complex circuit. The objective of the project, of which this work is part, is trying to solve this problem through the engineering of a multicellular behaviour in prokaryotic cells. This system will introduce a cooperative behaviour that will allow to implement complex functionalities, that can’t be obtained with a single cell. In particular the goal is to implement the Leader Election, this procedure has been firstly devised in the field of distributed computing, to identify the process that allow to identify a single process as organizer and coordinator of a series of tasks assigned to the whole population. The election of the Leader greatly simplifies the computation providing a centralized control. Further- more this system may even be useful to evolutionary studies that aims to explain how complex organisms evolved from unicellular systems. The work presented here describes, in particular, the design and the experimental characterization of a component of the circuit that solves the Leader Election problem. This module, composed of an hybrid promoter and a gene, is activated in the non-leader cells after receiving the signal that a leader is present in the colony. The most important element, in this case, is the hybrid promoter, it has been realized in different versions, applying the heuristic rules stated in [22], and their activity has been experimentally tested. The objective of the experimental characterization was to test the response of the genetic circuit to the introduction, in the cellular environment, of particular molecules, inducers, that can be considered inputs of the system. The desired behaviour is similar to the one of a logic AND gate in which the exit, represented by the luminous signal produced by a fluorescent protein, is one only in presence of both inducers. The robustness and the stability of this behaviour have been tested by changing the concentration of the input signals and building dose response curves. From these data it is possible to conclude that the analysed constructs have an AND-like behaviour over a wide range of inducers’ concentrations, even if it is possible to identify many differences in the expression profiles of the different constructs. This variability accounts for the fact that the input and the output signals are continuous, and so their binary representation isn’t able to capture the complexity of the behaviour. The module of the circuit that has been considered in this analysis has a fundamental role in the realization of the intercellular communication system that is necessary for the cooperative behaviour to take place. For this reason, the second phase of the characterization has been focused on the analysis of the signal transmission. In particular, the interaction between this element and the one that is responsible for emitting the chemical signal has been tested. The desired behaviour is still similar to a logic AND, since, even in this case, the exit signal is determined by the hybrid promoter activity. The experimental results have demonstrated that the systems behave correctly, even if there is still a substantial variability between them. The dose response curves highlighted that stricter constrains on the inducers concentrations need to be imposed in order to obtain a clear separation between the two levels of expression. In the conclusive chapter the DNA sequences of the hybrid promoters are analysed, trying to identify the regulatory elements that are most important for the determination of the gene expression. Given the available data it wasn’t possible to draw definitive conclusions. In the end, few considerations on promoter engineering and complex circuits realization are presented. This section aims to briefly recall some of the problems outlined in the introduction and provide a few possible solutions.