The Role of Molecular Conformation and Polarizable Embedding for One- and Two-Photon Absorption of Disperse Orange 3 in Solution

Solvent effects on the one- and two-photon absorption (IPA and 2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studied using a discrete polarizable embedding (PE) response theory. The scheme comprises a quantum region containing the chromophore and an atomically granulated classical region for the solvent accounting for full interactions within and between the two regions. Either classical molecular dynamics (MD) or hybrid Car-Parrinello (CP) quantum/classical (QM/MM) molecular dynamics simulations are employed to describe the solvation of DO3 in DMSO, allowing for an analysis of the effect of the intermolecular short-range repulsion, long-range attraction, and electrostatic interactions on the conformational changes of the chromophore and also the effect of the solute-solvent polarization. PE linear response calculations are performed to verify the character, solvatochromic shift, and overlap of the two lowest energy transitions responsible for the linear absorption spectrum of DO3 in DMSO in the visible spectral region. Results of the PE linear and quadratic response calculations, performed using uncorrelated solute-solvent configurations sampled from either the classical or hybrid CP QM/MM MD simulations, are used to estimate the width of the line shape function of the two electronic lowest energy excited states, which allow a prediction of the 2PA cross-sections without the use of empirical parameters. Appropriate exchange-correlation functionals have been employed in order to describe the charge-transfer process following the electronic transitions of the chromophore in solution.

Influence of the network modifier on the characteristics of MSnO3 (M=Sr and Ca) thin films synthesized by chemical solution deposition

CaSnO3 and SrSnO3 alkaline earth stannate thin films were prepared by chemical solution deposition using the polymeric precursor method on various single crystal substrates (R- and C-sapphire and 100-SrTiO3) at different temperatures. The films were characterized by X-ray diffraction (θ-2θ, ω- and φ-scans), field emission scanning electron microscopy, atomic force microscopy, micro-Raman spectroscopy and photoluminescence. Epitaxial SrSnO3 and CaSnO3 thin films were obtained on SrTiO3 with a high crystalline quality. The long-range symmetry promoted a short-range disorder which led to photoluminescence in the epitaxial films. In contrast, the films deposited on sapphire exhibited a random polycrystalline growth with no meaningful emission regardless of the substrate orientation. The network modifier (Ca or Sr) and the substrate (sapphire or SrTiO3) influenced the crystallization process and/or the microstructure. Higher is the tilts of the SnO6 octahedra, as in CaSnO3, higher is the crystallization temperature, which changed also the nucleation/grain growth process.

Dynamical aspects of atmospheric data assimilation in the tropics

A faithful depiction of the tropical atmosphere requires three-dimensional sets of observations. Despite the increasing amount of observations presently available, these will hardly ever encompass the entire atmosphere and, in addition, observations have errors. Additional (background) information will always be required to complete the picture. Valuable added information comes from the physical laws governing the flow, usually mediated via a numerical weather prediction (NWP) model. These models are, however, never going to be error-free, why a reliable estimate of their errors poses a real challenge since the whole truth will never be within our grasp. The present thesis addresses the question of improving the analysis procedures for NWP in the tropics. Improvements are sought by addressing the following issues: - the efficiency of the internal model adjustment, - the potential of the reliable background-error information, as compared to observations, - the impact of a new, space-borne line-of-sight wind measurements, and - the usefulness of multivariate relationships for data assimilation in the tropics. Most NWP assimilation schemes are effectively univariate near the equator. In this thesis, a multivariate formulation of the variational data assimilation in the tropics has been developed. The proposed background-error model supports the mass-wind coupling based on convectively-coupled equatorial waves. The resulting assimilation model produces balanced analysis increments and hereby increases the efficiency of all types of observations. Idealized adjustment and multivariate analysis experiments highlight the importance of direct wind measurements in the tropics. In particular, the presented results confirm the superiority of wind observations compared to mass data, in spite of the exact multivariate relationships available from the background information. The internal model adjustment is also more efficient for wind observations than for mass data. In accordance with these findings, new satellite wind observations are expected to contribute towards the improvement of NWP and climate modeling in the tropics. Although incomplete, the new wind-field information has the potential to reduce uncertainties in the tropical dynamical fields, if used together with the existing satellite mass-field measurements. The results obtained by applying the new background-error representation to the tropical short-range forecast errors of a state-of-art NWP model suggest that achieving useful tropical multivariate relationships may be feasible within an operational NWP environment.

Transcriptional regulation of human mu-opioid receptor gene: functional characterization of activating and inhibitory transcription factors

The organization of the nervous and immune systems is characterized by obvious differences and striking parallels. Both systems need to relay information across very short and very long distances. The nervous system communicates over both long and short ranges primarily by means of more or less hardwired intercellular connections, consisting of axons, dendrites, and synapses. Longrange communication in the immune system occurs mainly via the ordered and guided migration of immune cells and systemically acting soluble factors such as antibodies, cytokines, and chemokines. Its short-range communication either is mediated by locally acting soluble factors or transpires during direct cell–cell contact across specialized areas called “immunological synapses” (Kirschensteiner et al., 2003). These parallels in intercellular communication are complemented by a complex array of factors that induce cell growth and differentiation: these factors in the immune system are called cytokines; in the nervous system, they are called neurotrophic factors. Neither the cytokines nor the neurotrophic factors appear to be completely exclusive to either system (Neumann et al., 2002). In particular, mounting evidence indicates that some of the most potent members of the neurotrophin family, for example, nerve growth factor (NGF) and brainderived neurotrophic factor (BDNF), act on or are produced by immune cells (Kerschensteiner et al., 1999) There are, however, other neurotrophic factors, for example the insulin-like growth factor-1 (IGF-1), that can behave similarly (Kermer et al., 2000). These factors may allow the two systems to “cross-talk” and eventually may provide a molecular explanation for the reports that inflammation after central nervous system (CNS) injury has beneficial effects (Moalem et al., 1999). In order to shed some more light on such a cross-talk, therefore, transcription factors modulating mu-opioid receptor (MOPr) expression in neurons and immune cells are here investigated. More precisely, I focused my attention on IGF-I modulation of MOPr in neurons and T-cell receptor induction of MOPr expression in T-lymphocytes. Three different opioid receptors [mu (MOPr), delta (DOPr), and kappa (KOPr)] belonging to the G-protein coupled receptor super-family have been cloned. They are activated by structurallyrelated exogenous opioids or endogenous opioid peptides, and contribute to the regulation of several functions including pain transmission, respiration, cardiac and gastrointestinal functions, and immune response (Zollner and Stein 2007). MOPr is expressed mainly in the central nervous system where it regulates morphine-induced analgesia, tolerance and dependence (Mayer and Hollt 2006). Recently, induction of MOPr expression in different immune cells induced by cytokines has been reported (Kraus et al., 2001; Kraus et al., 2003). The human mu-opioid receptor gene (OPRM1) promoter is of the TATA-less type and has clusters of potential binding sites for different transcription factors (Law et al. 2004). Several studies, primarily focused on the upstream region of the OPRM1 promoter, have investigated transcriptional regulation of MOPr expression. Presently, however, it is still not completely clear how positive and negative transcription regulators cooperatively coordinate cellor tissue-specific transcription of the OPRM1 gene, and how specific growth factors influence its expression. IGF-I and its receptors are widely distributed throughout the nervous system during development, and their involvement in neurogenesis has been extensively investigated (Arsenijevic et al. 1998; van Golen and Feldman 2000). As previously mentioned, such neurotrophic factors can be also produced and/or act on immune cells (Kerschenseteiner et al., 2003). Most of the physiologic effects of IGF-I are mediated by the type I IGF surface receptor which, after ligand binding-induced autophosphorylation, associates with specific adaptor proteins and activates different second messengers (Bondy and Cheng 2004). These include: phosphatidylinositol 3-kinase, mitogen-activated protein kinase (Vincent and Feldman 2002; Di Toro et al. 2005) and members of the Janus kinase (JAK)/STAT3 signalling pathway (Zong et al. 2000; Yadav et al. 2005). REST plays a complex role in neuronal cells by differentially repressing target gene expression (Lunyak et al. 2004; Coulson 2005; Ballas and Mandel 2005). REST expression decreases during neurogenesis, but has been detected in the adult rat brain (Palm et al. 1998) and is up-regulated in response to global ischemia (Calderone et al. 2003) and induction of epilepsy (Spencer et al. 2006). Thus, the REST concentration seems to influence its function and the expression of neuronal genes, and may have different effects in embryonic and differentiated neurons (Su et al. 2004; Sun et al. 2005). In a previous study, REST was elevated during the early stages of neural induction by IGF-I in neuroblastoma cells. REST may contribute to the down-regulation of genes not yet required by the differentiation program, but its expression decreases after five days of treatment to allow for the acquisition of neural phenotypes. Di Toro et al. proposed a model in which the extent of neurite outgrowth in differentiating neuroblastoma cells was affected by the disappearance of REST (Di Toro et al. 2005). The human mu-opioid receptor gene (OPRM1) promoter contains a DNA sequence binding the repressor element 1 silencing transcription factor (REST) that is implicated in transcriptional repression. Therefore, in the fist part of this thesis, I investigated whether insulin-like growth factor I (IGF-I), which affects various aspects of neuronal induction and maturation, regulates OPRM1 transcription in neuronal cells in the context of the potential influence of REST. A series of OPRM1-luciferase promoter/reporter constructs were transfected into two neuronal cell models, neuroblastoma-derived SH-SY5Y cells and PC12 cells. In the former, endogenous levels of human mu-opioid receptor (hMOPr) mRNA were evaluated by real-time PCR. IGF-I upregulated OPRM1 transcription in: PC12 cells lacking REST, in SH-SY5Y cells transfected with constructs deficient in the REST DNA binding element, or when REST was down-regulated in retinoic acid-differentiated cells. IGF-I activates the signal transducer and activator of transcription-3 (STAT3) signaling pathway and this transcription factor, binding to the STAT1/3 DNA element located in the promoter, increases OPRM1 transcription. T-cell receptor (TCR) recognizes peptide antigens displayed in the context of the major histocompatibility complex (MHC) and gives rise to a potent as well as branched intracellular signalling that convert naïve T-cells in mature effectors, thus significantly contributing to the genesis of a specific immune response. In the second part of my work I exposed wild type Jurkat CD4+ T-cells to a mixture of CD3 and CD28 antigens in order to fully activate TCR and study whether its signalling influence OPRM1 expression. Results were that TCR engagement determined a significant induction of OPRM1 expression through the activation of transcription factors AP-1, NF-kB and NFAT. Eventually, I investigated MOPr turnover once it has been expressed on T-cells outer membrane. It turned out that DAMGO induced MOPr internalisation and recycling, whereas morphine did not. Overall, from the data collected in this thesis we can conclude that that a reduction in REST is a critical switch enabling IGF-I to up-regulate human MOPr, helping these findings clarify how human MOPr expression is regulated in neuronal cells, and that TCR engagement up-regulates OPRM1 transcription in T-cells. My results that neurotrophic factors a and TCR engagement, as well as it is reported for cytokines, seem to up-regulate OPRM1 in both neurons and immune cells suggest an important role for MOPr as a molecular bridge between neurons and immune cells; therefore, MOPr could play a key role in the cross-talk between immune system and nervous system and in particular in the balance between pro-inflammatory and pro-nociceptive stimuli and analgesic and neuroprotective effects.

Sphärische Bürsten in polymeren Schmelzen

Colloidal nanoparticles are additives to improve or modify several properties of thermoplastic or elastic polymers. Usually colloid-polymer mixtures show phase separation due to the depletion effect. The strategy to overcome this depletion demixing was to prepare surface-modified colloidal particles, which can be blended with linear polymer chains homogeneous. A successful synthesis strategy for the preparation of hairy nanospheres was developed by grafting polystyrene macromonomer chains onto polyorganosiloxane microgels. The number of hairs per particle with a core radius of approximately 10nm exceeded 150 hairs in all cases. The molecular weight of the hairs variied between 4000-18000g/mol.The compatibility of these hairy spheres mixed with linear polymer chains was investigated by AFM, TEM and SAXS. Homogeneous mixtures were found if the molecular weight of the polymer hairs on the particle surface is at least as large as the molecular weight of the matrix chains. If the chains are much shorter than the hairs, the colloidal hair corona is strongly swollen by the matrix polymer, leading to a long-range soft interparticle repulsion ('wet brush'). If hairs and chains are comparable in length, the corona shows much less volume swelling, leading to a short-range repulsive potential similar to hard sphere systems ('dry brush'). Polymerketten und Kolloidpartikel entmischen aufgrund von Depletion-Wechselwirkungen. Diese entropisch bedingte Entmischung konnte durch das Ankoppeln von Polymerhaaren verschiedenen Molekulargewichts auf die Kugeloberflächen der Kolloide bis zu hohen Konzentrationen vermieden werden. Zur Darstellung sphärischer Bürsten und haariger Tracerpartikel wurde eine neue Synthesestrategie ausgearbeitet und erfolgreich umgesetzt.Das Kompatibilitätsverhalten dieser sphärischen Bürsten in der Schmelze von Polymerketten als Matrix wurde mittels Elektronenmikroskopie und Kleinwinkelröntgenstreuung untersucht. Die Mischungen setzten sich aus sphärischen Bürsten und Matrixketten mit unterschiedlichen Molekulargewichten zusammen.Es zeigte sich, daß die Mischbarkeit entschieden durch das Verhältnis von Haarlänge zu Länge der Matrixketten beeinflußt wird.Aus den Untersuchungen des Relaxationsverhaltens mittels Rheologie und SAXS ergibt sich, daß das Konzept der 'dry brush'- und 'wet brush'-Systeme auf diese Mischungen übertragbar ist. Die Volumenquellung der Haarcorona durch die Matrixketten ist, wie die Experimente gezeigt haben, bereits im Fall von Polymeren mit relativ niedrigen Molekulargewichten zu beobachten. Sie ist umso stärker ausgeprägt, je größer das Längenverhältnis zwischen Polymerhaaren und Matrixketten ist. Die Quellung bedeutet eine Vergrößerung des effektiven Radius der Partikel und entspricht somit einer Erhöhung des effektiven Volumenbruchs. Dies führt zur Ausbildung einer höheren Ordnung und zu einem Einfrieren der Relaxation dieser strukturellen Ordnung führt.

Impatto della propagazione elettromagnetica sulle prestazioni delle reti M3N

Con il termine Smart Grid si intende una rete urbana capillare che trasporta energia, informazione e controllo, composta da dispositivi e sistemi altamente distribuiti e cooperanti. Essa deve essere in grado di orchestrare in modo intelligente le azioni di tutti gli utenti e dispositivi connessi al fine di distribuire energia in modo sicuro, efficiente e sostenibile. Questo connubio fra ICT ed Energia viene comunemente identificato anche con il termine Smart Metering, o Internet of Energy. La crescente domanda di energia e l’assoluta necessità di ridurre gli impatti ambientali (pacchetto clima energia 20-20-20 [9]), ha creato una convergenza di interessi scientifici, industriali e politici sul tema di come le tecnologie ICT possano abilitare un processo di trasformazione strutturale di ogni fase del ciclo energetico: dalla generazione fino all’accumulo, al trasporto, alla distribuzione, alla vendita e, non ultimo, il consumo intelligente di energia. Tutti i dispositivi connessi, diventeranno parte attiva di un ciclo di controllo esteso alle grandi centrali di generazione così come ai comportamenti dei singoli utenti, agli elettrodomestici di casa, alle auto elettriche e ai sistemi di micro-generazione diffusa. La Smart Grid dovrà quindi appoggiarsi su una rete capillare di comunicazione che fornisca non solo la connettività fra i dispositivi, ma anche l’abilitazione di nuovi servizi energetici a valore aggiunto. In questo scenario, la strategia di comunicazione sviluppata per lo Smart Metering dell’energia elettrica, può essere estesa anche a tutte le applicazioni di telerilevamento e gestione, come nuovi contatori dell’acqua e del gas intelligenti, gestione dei rifiuti, monitoraggio dell’inquinamento dell’aria, monitoraggio del rumore acustico stradale, controllo continuo del sistema di illuminazione pubblico, sistemi di gestione dei parcheggi cittadini, monitoraggio del servizio di noleggio delle biciclette, ecc. Tutto ciò si prevede possa contribuire alla progettazione di un unico sistema connesso, dove differenti dispositivi eterogenei saranno collegati per mettere a disposizione un’adeguata struttura a basso costo e bassa potenza, chiamata Metropolitan Mesh Machine Network (M3N) o ancora meglio Smart City. Le Smart Cities dovranno a loro volta diventare reti attive, in grado di reagire agli eventi esterni e perseguire obiettivi di efficienza in modo autonomo e in tempo reale. Anche per esse è richiesta l’introduzione di smart meter, connessi ad una rete di comunicazione broadband e in grado di gestire un flusso di monitoraggio e controllo bi-direzionale esteso a tutti gli apparati connessi alla rete elettrica (ma anche del gas, acqua, ecc). La M3N, è un’estensione delle wireless mesh network (WMN). Esse rappresentano una tecnologia fortemente attesa che giocherà un ruolo molto importante nelle futura generazione di reti wireless. Una WMN è una rete di telecomunicazione basata su nodi radio in cui ci sono minimo due percorsi che mettono in comunicazione due nodi. E’ un tipo di rete robusta e che offre ridondanza. Quando un nodo non è più attivo, tutti i rimanenti possono ancora comunicare tra di loro, direttamente o passando da uno o più nodi intermedi. Le WMN rappresentano una tipologia di rete fondamentale nel continuo sviluppo delle reti radio che denota la divergenza dalle tradizionali reti wireless basate su un sistema centralizzato come le reti cellulari e le WLAN (Wireless Local Area Network). Analogamente a quanto successo per le reti di telecomunicazione fisse, in cui si è passati, dalla fine degli anni ’60 ai primi anni ’70, ad introdurre schemi di rete distribuite che si sono evolute e man mano preso campo come Internet, le M3N promettono di essere il futuro delle reti wireless “smart”. Il primo vantaggio che una WMN presenta è inerente alla tolleranza alla caduta di nodi della rete stessa. Diversamente da quanto accade per una rete cellulare, in cui la caduta di una Base Station significa la perdita di servizio per una vasta area geografica, le WMN sono provviste di un’alta tolleranza alle cadute, anche quando i nodi a cadere sono più di uno. L'obbiettivo di questa tesi è quello di valutare le prestazioni, in termini di connettività e throughput, di una M3N al variare di alcuni parametri, quali l’architettura di rete, le tecnologie utilizzabili (quindi al variare della potenza, frequenza, Building Penetration Loss…ecc) e per diverse condizioni di connettività (cioè per diversi casi di propagazione e densità abitativa). Attraverso l’uso di Matlab, è stato quindi progettato e sviluppato un simulatore, che riproduce le caratteristiche di una generica M3N e funge da strumento di valutazione delle performance della stessa. Il lavoro è stato svolto presso i laboratori del DEIS di Villa Grifone in collaborazione con la FUB (Fondazione Ugo Bordoni).

Physikalische Eigenschaften kolloidaler Festkörper

In dieser Arbeit wird das Phasenverhalten fluid-kristallin und kristallin-amorph, die elastischen Eigenschaften, das Nukleationsverhalten und das diffusive Verhalten ladungsstabilisierter Kolloide aus sphärischen Polystyrol- und Polytetrafluorethylenpartikeln in wässerigen Dispersionsmitteln bei sehr geringem Fremdionengehalt systematisch untersucht. Die dazugehörigen Messungen werden an einer neuartigen selbstkonstruierten Kombinationslichtstreuapparatur durchgeführt, die die Meßmethoden der dynamischen Lichtstreuung, statischen Lichtstreuung und Torsionsresonanzspektroskopie in sich vereint. Die drei Meßmethoden sind optimal auf die Untersuchung kolloidaler Festkörper abgestimmt. Das elastische Verhalten der Festkörper kann sehr gut durch die Elastizitätstheorie atomarer Kristallsysteme beschrieben werden, wenn ein Debye-Hückel-Potential im Sinne des Poisson-Boltzmann-Cell Modells als Wechselwirkungspotential verwendet wird. Die ermittelten Phasengrenzen fluid-kristallin stehen erstmalig in guter Übereinstimmung mit Ergebnissen aus molekulardynamischen Simulationen, wenn die in der Torsionsresonanzspektroskopie bestimmte Wechselwirkungsenergie zu Grunde gelegt wird. Neben der Gleichgewichtsstruktur sind Aussagen zur Verfestigungskinetik möglich. Das gefundene Nukleationserhalten kann gut durch die klassische Nukleationstheorie beschrieben werden, wenn bei niedriger Unterkühlung der Schmelze ein Untergrund heterogener Keimung berücksichtigt wird. PTFE-Partikel zeigen auch bei hohen Konzentrationen nur geringfügige Mehrfachstreuung. Durch ihren Einsatz ist erstmals eine systematische Untersuchung des Glasübergangs in hochgeladenen ladungsstabilisierten Systemen möglich. Ladungsstabilisierte Kolloide unterscheiden sich vor allem durch ihre extreme Kristallisationstendenz von früher untersuchten Hartkugelsystemen. Bei hohen Partikelkonzentrationen (Volumenbrüche größer 10 Prozent) kann ein glasartiger Festkörper identifiziert werden, dessen physikalisches Verhalten die Existenz eines Bernalglases nahe legt. Der Glasübergang ist im Vergleich mit den in anderen kolloidalen Systemen und atomaren Systemen beobachteten Übergängen von sehr unterschiedlichem Charakter. Im verwendeten PTFE-System ist auf Grund der langreichweitigen stark repulsiven Wechselwirkung kein direkter Zugang des Glaszustandes aus der übersättigten Schmelze möglich. Der amorphe Festkörper entsteht hier aus einer nanokristallinen Phase. Die Keimrate steigt im zugänglichen Meßbereich annähernd exponentiell mit der Partikelanzahldichte, so daß man feststellen kann, daß der Glaszustand nicht durch Unterdrückung der Nukleation, sondern durch eine Forcierung derselben erreicht wird.

Strukturbildungsverhalten kettensteifer Polyelektrolyte in wässrigen Lösungen am Beispiel von Poly(para-phenylen)sulfonat

An einer Vielzahl biogener Polyelektrolyte, wie z.B. den Nukleinsäuren DNA und RNA sowie Proteinen, ist die Ausbildung von Strukturhierarchien durch Selbstorganisation von Strukturelementen zu beobachten. Dabei wird das Strukturbildungsverhalten durch eine Kopplung von Wechselwirkungen auf verschiedenen Längenskalen, den kurzreichweitigen ausgeschlossenen Volumen und den langreichweitigen elektrostatischen Wechselwirkungen (Coulomb-Wechselwirkungen), die wiederum durch eine Vielzahl mikroskopische Parameter (z.B. Konformation) beeinflusst werden, bestimmt. Durch diese Komplexität ist es nicht möglich, den für die Strukturbildung hochgeladener Systeme bedeutsamen Beitrag der elektrostatischen Wechselwirkungen isoliert zu betrachten. Aus diesem Grund werden zur Aufklärung von Wechselwirkungs- und Strukturbildungsmechanismen vereinfachte Modell-Systeme herangezogen. Eine Möglichkeit besteht in der Verwendung synthetischer, kettensteifer Polyelektrolyte. Im Rahmen dieser Arbeit wurde das Aggregationsverhalten wässriger Lösungen dodecylsubstituierter Poly(para-phenylen)sulfonate (PPPS) sowie die Beeinflussung der Strukturbildung durch verschiedene Parameter charakterisiert. Als Einflussparameter wurden einerseits die Gegenion-Spezies und andererseits die Temperatur- und Konzentrations-Abhängigkeit untersucht. Hierzu wurden wässrige Lösungen der freien Säuren der PPPS mit Molekulargewichten zwischen MW = 18 kg/mol bis 58 kg/mol mittels Licht-, Röntgen- und Neutronenstreuung sowie durch Licht-, Polarisations-, Transmissionselektronen- und Rasterkraftmikroskopie in einem Konzentrationsbereich von 0,0008 < c < 1,1 g/L untersucht.

Spin polarised Heusler compounds

In der vorliegenden Dissertation dient ein einfaches Konzept zur Systematisierung der Suche nach neuen Materialien mit hoher Spinpolarisation. Dieses Konzept basiert auf zwei semi-empirischen Modellen. Zum einen kann die Slater-Pauling Regel zur Abschätzung magnetischer Momente verwendet werden. Dieses Modell wird dabei durch Rechnungen zur elektronischen Struktur unterstützt. Das zweites Modell kann insbesondere für die Co2YZ Heusler Verbindungen beim Vergleich ihrer magnetischen Eigenschaften gefunden werden. Für diese Verbindungen ergibt sich eine scheinbare lineare Abhängigkeit der Curie-Temperatur beim Auftragen als Funktion des magnetischen Momentes. Angeregt durch diese Modelle wurde die Heusler Verbindung Co2FeSi nochmals detailliert im Hinblick auf ihre geometrische und magnetische Struktur hin untersucht. Als Methoden dienten dabei die Pulver-Röntgenbeugung, die EXAFS Spektroskopie, Röntgen Absorptions- and Mößbauer Spektroskopie sowie Hoch- und Tieftemperatur Magnetometrie, XMCD and DSC. Die Messungen zeigten, dass es sich bei Co2FeSi um das Material mit dem höchsten magnetischen Moment (6 B) und der höchsten Curie Temperatur (1100 K) sowohl in der Klasse der Heusler Verbindungen als auch in der Klasse der halbmetallischen Ferromagnete handelt. Zusätzlich werden alle experimentellen Ergebnisse durch detaillierte Rechnungen zur elektronischen Struktur unterstützt. Die gleichen Konzepte wurden verwendet, um die Eigenschaften der Heusler Verbindung Co2Cr1-xFexAl vorherzusagen. Die elektronische Struktur und die spektroskopischen Eigenschaften wurden mit der voll-relativistischen Korringa-Kohn-Rostocker Methode berechnet, unter Verwendung kohärenter Potentialnäherungen um der zufälligen Verteilung von Cr und Fe Atomen sowie zufälliger Unordnung Rechnung zu tragen. Magnetische Effekte wurden durch die Verwendung Spin-abhängiger Potentiale im Rahmen der lokalen Spin-Dichte-Näherung mit eingeschlossen. Die strukturellen und chemischen Eigenschaften der quaternären Heusler Verbindung Co2Cr1-xFexAl wurden an Pulver und Bulkproben gemessen. Die Fernordnung wurde mit der Pulver Röntgenbeugung und Neutronenbeugung untersucht, während die Nahordnung mit der EXAFS Spektroskopie aufgeklärt wurde. Die magnetische Struktur von Pulver und Bulkproben wurde mitttels 57Fe-Mößbauer Spektroskopie gemessen. Die chemische Zusammensetzung wurde durch XPS analysiert. Die Ergebnisse dieser Methoden wurden verglichen, um eine Einsicht in die Unterschiede zwischen Oberflächen und Volumeneigenschaften zu erlangen sowie in das Auftreten von Fehlordnung in solchen Verbindungen. Zusätzlich wurde XMCD an den L3,2 Kanten von Co, Fe, and Cr gemessen, um die elementspezifischen magnetischen Momente zu bestimmen. Rechnungen und Messungen zeigen dabei eine Zunahme des magnetischen Momentes bei steigendem Fe-Anteil. Resonante Photoemission mit weicher Röntgenstrahlung sowie Hochenergie Photoemission mit harter Röntgenstrahlung wurden verwendet, um die Zustandsdichte der besetzten Zustände in Co2Cr0.6Fe0.4Al zu untersuchen. Diese Arbeit stellt außerdem eine weitere, neue Verbindung aus der Klasse der Heusler Verbindungen vor. Co2CrIn ist L21 geordnet, wie Messungen mittels Pulver Röntgenbeugung zeigen. Die magnetischen Eigenschaften wurden mit magnetometrisch bestimmt. Co2CrIn ist weichmagnetisch mit einer Sättigungsmagnetisierung von 1.2B bei 5 K. Im Gegensatz zu den bereits oben erwähnten Co2YZ Heusler Verbindungen ist Co2CrIn kein halbmetallischer Ferromagnet. Im Rahmen dieser Arbeit wird weiterhin eine Regel zur Vorhersage von halbmetallischen komplett kompensierten Ferrimagneten in der Klasse der Heusler Verbindungen vorgestellt. Dieses Konzept resultiert aus der Kombination der Slater-Pauling Regel mit der Kübler-Regel. Die Kübler Regel besagt, dass Mn auf der Y Position zu einem hoch lokalisierten magnetischen Moment tendiert. Unter Verwendung dieses neuen Konzeptes werden für einige Kandidaten in der Klasse der Heusler Verbindungen die Eigenschaft des halbmetallischen komplett kompensierten Ferrimagnetismus vorhergesagt. Die Anwendung dieses Konzeptes wird anhand von Rechnungen zur elektronischen Struktur bestätigt.

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

Fiber-Optic Technologies for Wireline and Wireless In-building Networks

This doctoral dissertation aims to establish fiber-optic technologies overcoming the limiting issues of data communications in indoor environments. Specific applications are broadband mobile distribution in different in-building scenarios and high-speed digital transmission over short-range wired optical systems. Two key enabling technologies are considered: Radio over Fiber (RoF) techniques over standard silica fibers for distributed antenna systems (DAS) and plastic optical fibers (POFs) for short-range communications. Hence, the objectives and achievements of this thesis are related to the application of RoF and POF technologies in different in-building scenarios. On one hand, a theoretical and experimental analysis combined with demonstration activities has been performed on cost-effective RoF systems. An extensive modeling on modal noise impact both on linear and non-linear characteristics of RoF link over silica multimode fiber has been performed to achieve link design rules for an optimum choice of the transmitter, receiver and launching technique. A successful transmission of Long Term Evolution (LTE) mobile signals on the resulting optimized RoF system over silica multimode fiber employing a Fabry-Perot LD, central launch technique and a photodiode with a built-in ball lens was demonstrated up to 525m with performances well compliant with standard requirements. On the other hand, digital signal processing techniques to overcome the bandwidth limitation of POF have been investigated. An uncoded net bit-rate of 5.15Gbit/s was obtained on a 50m long POF link employing an eye-safe transmitter, a silicon photodiode, and DMT modulation with bit and power loading algorithm. With the insertion of 3x2N quadrature amplitude modulation constellation formats, an uncoded net-bit-rate of 5.4Gbit/s was obtained on a 50 m long POF link employing an eye-safe transmitter and a silicon avalanche photodiode. Moreover, simultaneous transmission of baseband 2Gbit/s with DMT and 200Mbit/s with an ultra-wideband radio signal has been validated over a 50m long POF link.

Statistische Betrachtungen und mößbauerspektroskopische Untersuchungen von Ordnungszuständen in Biotiten

Im Mittelpunkt der vorliegenden Arbeit standen Untersuchungen zu strukturellen Ordnungs- und Unordnungsphänomenen an natürlichen, substitutionellen Mischkristallen. Aufgrund der enormen Vielfalt an potentiellen Austauschpartnern wurden hierfür Vertreter der Biotit-Mischkristallreihe "Phlogopit-Annit" ausgewählt. Ihr modulartiger Aufbau ermöglichte die gezielte Beschreibung von Verteilungsmustern anionischer und kationischer Merkmalsträger innerhalb der Oktaederschicht der Biotit-Mischkristalle. Basierend auf der postulierten Bindungsaffinität zwischen Mg2+ und F- einerseits und Fe2+ und OH- andererseits, wurde die strukturelle Separation einer Fluor-Phlogopit-Komponente als primäre Ausprägungsform des Mg/F-Ordnungsprinzips abgeleitet. Im Rahmen dieser Modellvorstellung koexistieren im makroskopisch homogenen Biotit-Mischkristall Domänen zweier chemisch divergenter Phasen nebeneinander: Eine rein Mg2+/F- - führende Phlogopit-Phase und eine Wirtskristallphase, die mit fortschreitender Separation bzw. Entmischung der erstgenannten Phase sukzessive reicher an einer hydroxylführenden eisenreichen Annit-Komponente wird. Zwecks numerischer Beschreibung diverser Stadien der Entmischungsreaktion wurden die Begriffe der "Relativen" und "Absoluten Domänengröße" eingeführt. Sie stellen ein quantitatives Maß zur Beurteilung der diskutierten Ordnungsphänomene dar. Basierend auf einem sich stetig ändernden Chemismus der Wirtskristallphase kann jeder Übergangszustand zwischen statistischer Verteilung und vollständiger Ordnung durch das korrespondierende Verteilungsmuster der interessierenden Merkmalsträger ( = Nahordnungskonfiguration und Besetzungswahrscheinlichkeit) charakterisiert und beschrieben werden. Durch mößbauerspektroskopische Untersuchungen konnten die anhand der entwickelten Modelle vorhergesagten Ausprägungsformen von Ordnungs-/Unordnungsphänomenen qualitativ und quantitativ verifiziert werden. Es liessen sich hierbei zwei Gruppen von Biotit-Mischkristallen unterscheiden. Eine erste Gruppe, deren Mößbauer-Spektren durch den OH/F-Chemismus als dominierendes Differenzierungsmerkmal geprägt wird, und eine zweite Gruppe, deren Mößbauer-Spektren durch Gruppierungen von höherwertigen Kationen und Vakanzen ( = Defektchemie) geprägt wird. Auf der Basis von Korrelationsdiagrammen, die einen numerischen und graphischen Bezug zwischen absoluter und relativer Domänengröße einerseits und experimentell zugänglichem Mößbauer-Parameter A (= relativer Flächenanteil, korrespondierend mit der Besetzungswahrscheinlichkeit einer bestimmten Nahordnungs-konstellation) andererseits herstellen, konnten für die erste Gruppe die Volumina der beiden miteinander koexistierenden Komponenten "Hydroxyl-Annit reicher Wirtskristall" und "Fluor-Phlogopit" exakt quantifiziert werden. Das Spektrum der untersuchten Proben umfasste hierbei Kristallspezies, die einerseits durch geringe bis mittlere Mg2+/F- - bzw. Fe2+/OH- -Ordnungsgrade gekennzeichnet sind, andererseits eine nahezu vollständige Ordnung der interessierenden Merkmalsträger Mg2+, Fe2+, OH- und F- widerspiegeln. Desweiteren konnte der Nachweis geführt werden, dass für ausgewählte Proben eine quantitative Bestimmung der Defektvolumina möglich ist.

Genome characterization through a mathematical model of the genetic code: an analysis of the whole chromosome 1 of A. thaliana

The objective of this work is to characterize the genome of the chromosome 1 of A.thaliana, a small flowering plants used as a model organism in studies of biology and genetics, on the basis of a recent mathematical model of the genetic code. I analyze and compare different portions of the genome: genes, exons, coding sequences (CDS), introns, long introns, intergenes, untranslated regions (UTR) and regulatory sequences. In order to accomplish the task, I transformed nucleotide sequences into binary sequences based on the definition of the three different dichotomic classes. The descriptive analysis of binary strings indicate the presence of regularities in each portion of the genome considered. In particular, there are remarkable differences between coding sequences (CDS and exons) and non-coding sequences, suggesting that the frame is important only for coding sequences and that dichotomic classes can be useful to recognize them. Then, I assessed the existence of short-range dependence between binary sequences computed on the basis of the different dichotomic classes. I used three different measures of dependence: the well-known chi-squared test and two indices derived from the concept of entropy i.e. Mutual Information (MI) and Sρ, a normalized version of the “Bhattacharya Hellinger Matusita distance”. The results show that there is a significant short-range dependence structure only for the coding sequences whose existence is a clue of an underlying error detection and correction mechanism. No doubt, further studies are needed in order to assess how the information carried by dichotomic classes could discriminate between coding and noncoding sequence and, therefore, contribute to unveil the role of the mathematical structure in error detection and correction mechanisms. Still, I have shown the potential of the approach presented for understanding the management of genetic information.

Ex situ X-­Ray absorption study of Li-­rich layered cathode material Li[Li0.2Mn0.56Ni0.16Co0.08]O2

The Li-rich layered transition metal oxides (LLOs) Li2MnO3-LiMO2 (M=Mn, Co, Ni, etc.) have drawn considerable attention as cathode materials for rechargeable lithium batteries. They generate large reversible capacities but the fundamental reaction mechanism and structural perturbations during cycling remain controversial. In the present thesis, ex situ X-ray absorption spectroscopy (XAS) measurements were performed on Li[Li0.2Mn0.56Ni0.16Co0.08]O2 at different stage of charge during electrochemical oxidation/reduction. K-edge spectra of Co, Mn and Ni were recorded through a voltage range of 3.7-4.8V vs. Li/Li+, which consist of X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). Oxidation states during initial charge were discussed based on values from literature as well as XANES analysis. Information about bond distance, coordination number as well as corresponding Debye-Waller factor were extracted from Gnxas analysis of raw data in the EXAFS region. The possibility of oxygen participation in the initial charge was discussed. Co and Ni prove to take part in the oxidation/reduction process while Mn remain in the tetravalent state. The cathode material appears to retain good structural short-range order during charge-discharge. A resemblance of the pristine sample and sample 4 was discovered which was firstly reported for similar compounds.

New sensing platforms based on nanoscopic devices for probing protein-membrane interactions

A novel nanosized and addressable sensing platform based on membrane coated plasmonic particles for detection of protein adsorption using dark field scattering spectroscopy of single particles has been established. To this end, a detailed analysis of the deposition of gold nanorods on differently functionalized substrates is performed in relation to various factors (such as the pH, ionic strength, concentration of colloidal suspension, incubation time) in order to find the optimal conditions for obtaining a homogenous distribution of particles at the desired surface number density. The possibility of successfully draping lipid bilayers over the gold particles immobilized on glass substrates depends on the careful adjustment of parameters such as membrane curvature and adhesion properties and is demonstrated with complementary techniques such as phase imaging AFM, fluorescence microscopy (including FRAP) and single particle spectroscopy. The functionality and sensitivity of the proposed sensing platform is unequivocally certified by the resonance shifts of the plasmonic particles that were individually interrogated with single particle spectroscopy upon the adsorption of streptavidin to biotinylated lipid membranes. This new detection approach that employs particles as nanoscopic reporters for biomolecular interactions insures a highly localized sensitivity that offers the possibility to screen lateral inhomogeneities of native membranes. As an alternative to the 2D array of gold nanorods, short range ordered arrays of nanoholes in optically transparent gold films or regular arrays of truncated tetrahedron shaped particles are built by means of colloidal nanolithography on transparent substrates. Technical issues mainly related to the optimization of the mask deposition conditions are successfully addressed such that extended areas of homogenously nanostructured gold surfaces are achieved. Adsorption of the proteins annexin A1 and prothrombin on multicomponent lipid membranes as well as the hydrolytic activity of the phospholipase PLA2 were investigated with classical techniques such as AFM, ellipsometry and fluorescence microscopy. At first, the issues of lateral phase separation in membranes of various lipid compositions and the dependency of the domains configuration (sizes and shapes) on the membrane content are addressed. It is shown that the tendency for phase segregation of gel and fluid phase lipid mixtures is accentuated in the presence of divalent calcium ions for membranes containing anionic lipids as compared to neutral bilayers. Annexin A1 adsorbs preferentially and irreversibly on preformed phosphatidylserine (PS) enriched lipid domains but, dependent on the PS content of the bilayer, the protein itself may induce clustering of the anionic lipids into areas with high binding affinity. Corroborated evidence from AFM and fluorescence experiments confirm the hypothesis of a specifically increased hydrolytic activity of PLA2 on the highly curved regions of membranes due to a facilitated access of lipase to the cleavage sites of the lipids. The influence of the nanoscale gold surface topography on the adhesion of lipid vesicles is unambiguously demonstrated and this reveals, at least in part, an answer for the controversial question existent in the literature about the behavior of lipid vesicles interacting with bare gold substrates. The possibility of formation monolayers of lipid vesicles on chemically untreated gold substrates decorated with gold nanorods opens new perspectives for biosensing applications that involve the radiative decay engineering of the plasmonic particles.