Automatic code generation: from process algebraic architectural descriptions to multithreaded java programs

Process algebraic architectural description languages provide a formal means for modeling software systems and assessing their properties. In order to bridge the gap between system modeling and system im- plementation, in this thesis an approach is proposed for automatically generating multithreaded object-oriented code from process algebraic architectural descriptions, in a way that preserves – under certain assumptions – the properties proved at the architectural level. The approach is divided into three phases, which are illustrated by means of a running example based on an audio processing system. First, we develop an architecture-driven technique for thread coordination management, which is completely automated through a suitable package. Second, we address the translation of the algebraically-specified behavior of the individual software units into thread templates, which will have to be filled in by the software developer according to certain guidelines. Third, we discuss performance issues related to the suitability of synthesizing monitors rather than threads from software unit descriptions that satisfy specific constraints. In addition to the running example, we present two case studies about a video animation repainting system and the implementation of a leader election algorithm, in order to summarize the whole approach. The outcome of this thesis is the implementation of the proposed approach in a translator called PADL2Java and its integration in the architecture-centric verification tool TwoTowers.

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Self assembled monolayers for engineering of structured inorganic materials in the micrometer and submicrometer range

Deutsch:In der vorliegenden Arbeit konnten neue Methoden zur Synthese anorganischer Materialien mit neuartiger Architektur im Mikrometer und Nanometer Maßstab beschrieben werden. Die zentrale Rolle der Formgebung basiert dabei auf der templatinduzierten Abscheidung der anorganischen Materialien auf selbstorganisierten Monoschichten. Als Substrate eignen sich goldbedampfte Glasträger und Goldkolloide, die eine Mittelstellung in der Welt der Atome bzw. Moleküle und der makroskopischen Welt der ausgedehnten Festkörper einnehmen. Auf diesen Substraten lassen sich Thiole zu einer monomolekularen Schicht adsorbieren und damit die Oberflächeneigenschaften des Substrates ändern. Ein besonderer Schwerpunkt bei dieser Arbeit stellt die Synthese speziell auf die Bedürfnisse der jeweiligen Anwendung ausgerichteten Thiole dar.Im ersten Teil der Arbeit wurden goldbedampfte Glasoberflächen als Template verwendet. Die Abscheidung von Calciumcarbonat wurde in Abhängigkeit der Schichtdicke der adsorbierten Monolage untersucht. Aragonit, eine der drei Hauptphasen des Calciumcarbonat Systems, wurde auf polyaromatischen Amid - Oberflächen mit Schichtdicken von 5 - 400 nm Dicke unter milden Bedingung abgeschieden. Die einstellbaren Parameter waren dabei die Kettenlänge des Polymers, der w-Substituent, die Bindung an die Goldoberfläche über Verwendung verschiedener Aminothiole und die Kristallisationstemperatur. Die Schichtdickeneinstellung der Polymerfilme erfolgte hierbei über einen automatisierten Synthesezyklus.Titanoxid Filme konnten auf Oberflächen strukturiert werden. Dabei kam ein speziell synthetisiertes Thiol zum Einsatz, das die Funktionalität einer Styroleinheit an der Oberflächen Grenze als auch eine Möglichkeit zur späteren Entfernung von der Oberfläche in sich vereinte. Die PDMS Stempeltechnik erzeugte dabei Mikrostrukturen auf der Goldoberfläche im Bereich von 5 bis 10 µm, die ihrerseits über die Polymerisation und Abscheidung des Polymers in den Titanoxid Film überführt werden konnten. Drei dimensionale Strukturen wurden über Goldkolloid Template erhalten. Tetraethylenglykol konnte mit einer Thiolgruppe im Austausch zu einer Hydroxylgruppe monofunktionalisiert werden. Das erhaltene Molekül wurde auf kolloidalem Gold selbstorganisiert; es entstand dabei ein wasserlösliches Goldkolloid. Die Darstellung erfolgte dabei in einer Einphasenreaktion. Die so erhaltenen Goldkolloide wurden als Krstallisationstemplate für die drei dimensionale Abscheidung von Calciumcarbonat verwendet. Es zeigte sich, dass Glykol die Kristallisation bzw. den Habitus des krsitalls bei niedrigem pH Wert modifiziert. Bei erhöhtem pH Wert (pH = 12) jedoch agieren die Glykol belegten Goldkolloide als Template und führen zu sphärisch Aggregaten. Werden Goldkolloide langkettigen Dithiolen ausgesetzt, so führt dies zu einer Aggregation und Ausfällung der Kolloide aufgrund der Vernetzung mehrer Goldkolloide mit den Thiolgruppen der Alkyldithiole. Zur Vermeidung konnte in dieser Arbeit ein halbseitig geschütztes Dithiol synthetisiert werden, mit dessen Hilfe die Aggregation unterbunden werden konnte. Das nachfolgende Entschützten der Thiolfunktion führte zu Goldkolloiden, deren Oberfläche Thiol funktionalisiert werden konnte. Die thiolaktiven Goldkolloide fungierten als template für die Abscheidung von Bleisulfid aus organisch/wässriger Lösung. Die Funktionsweise der Schutzgruppe und die Entschützung konnte mittels Plasmonenresonanz Spektroskopie verdeutlicht werden. Titanoxid / Gold / Polystyrol Komposite in Röhrenform konnten synthetisiert werden. Dazu wurde ein menschliches Haar als biologisches Templat für die Formgebung gewählt.. Durch Bedampfung des Haares mit Gold, Assemblierung eines Stryrolmonomers, welches zusätzlich eine Thiolfunktionalität trug, Polymerisation auf der Oberfläche, Abscheidung des Titanoxid Films und anschließendem Auflösen des biologischen Templates konnte eine Röhrenstruktur im Mikrometer Bereich dargestellt werden. Goldkolloide fungierten in dieser Arbeit nicht nur als Kristallisationstemplate und Formgeber, auch sie selbst wurden dahingehend modifiziert, dass sie drahtförmige Agglormerate im Nanometerbereich ausbilden. Dazu wurden Template aus Siliziumdioxid benutzt. Zum einen konnten Nanoröhren aus amorphen SiO2 in einer Sol Gel Methode dargestellt werden, zum anderen bediente sich diese Arbeit biologischer Siliziumoxid Hohlnadeln aus marinen Schwämmen isoliert. Goldkolloide wurden in die Hohlstrukturen eingebettet und die Struktur durch Ausbildung von Kolloid - Thiol Netzwerken mittels Dithiol Zugabe gefestigt. Die Gold-Nanodrähte im Bereich von 100 bis 500 nm wurden durch Auflösen des SiO2 - Templates freigelegt.

Synthese und Strukturierung von funktionalisierten Oligothiophenen

AbstractIn this thesis t-BOC and methacrylate functionalisedoligothiophenes with 3 – 5 thiophene units where synthesizedby Stille coupling. The material was structured by methodslike stamping and photolithography.The polymerizability of the methacrylates was proved by thepolymerization in solution with AIBN and subsequent analysisby gel permeation chromatography and differential scanningcalorimetry. The conductivities of the doped polymer filmswere in the range published for oligothiophenes.The optical and electrochemical properties of the compoundswere measured and compared to known compounds.The cleavage of the t-BOC groups was followed bythermogravimetry and infrared spectroscopy. The cleavagetemperature can be lowered by up to 100 °C by the use ofphoto acid generators. The cleavage is complete after 2hours annealing.The methacrylates were structured by microinjection mouldingin capillaries (MIMIC), stamping with soft silicone moulds,filling of patterned substrates and preperation of an opalreplica. By MIMIC line patterns with 5- 50 µm line widthswere obtained. The stamping succeeded in structures with 500nm line width only, on which liquid crystals wereorientated. This shows the possible application asorientation layers in LED’s with polarized emission. Withsilica opal templates the three-dimensional structuring ofthe oligomers succeeded.ZusammenfassungIn dieser Arbeit wurden neue funktionalisierteOligothiophene hergestellt und unter Anwendung verschiedenerVerfahren wie Stempeltechniken oder Photolithographiestrukturiert. Dazu wurden Oligothiophene mit drei bis fünfThiopheneinheiten durch Stille-Kupplung synthetisiert. Alsfunktionelle Gruppen wurden t-BOC-Ester undMethacrylsäureester eingeführt.Die Polymerisierbarkeit der Methacrylate wurde durch diePolymerisation mit AIBN in Lösung und anschließendeGelpermeationschromatographie und Differentialkalorimetrienachgewiesen. Die Leitfähigkeiten der dotierten Polymerfilmelagen im Bereich der für Oligothiophene bekannten Werte.Die optischen und elektrochemischen Eigenschaften derVerbindungen wurden untersucht und mit den Eigenschaftenbekannter Verbindungen verglichen. Die Abspaltung der t-BOC-Gruppen wurde thermogravimetrischund infrarotspektroskopisch verfolgt. Es wurde gezeigt, daßdie Abspaltungstemperatur durch den Zusatz einesPhotosäuregenerators um bis zu 100°C gesenkt wird und dieAbspaltung nach zweistündigem Tempern vollständig ist.Die methacrylatfunktionalisierten Verbindungen wurdenstrukturiert durch Micro Injection Moulding in Capillaries(MIMIC), Prägen mit weichen Silikonstempeln, Füllen vonstrukturierten Substraten und die Herstellung einerOpalreplika. Durch die Strukturierung mit MIMIC wurdenLinienstrukturen mit Linienbreiten von 5-50 µm erhalten.Durch Prägen wurden Strukturen mit Linienbreiten von nur 500nm erreicht, auf diesen gelang die Orientierung vonFlüssigkristallen. Dies zeigt die mögliche Anwendung alsOrientierungsschichten in Leuchtdioden mit polarisierterEmission. Durch die Verwendung von Siliziumoxidopalen alsTemplate gelang die dreidimensionale Strukturierung derOligomere.

Investigations of cooperative interactions in template induced crystallization processes and kinetic studies of nucleation and growth by small-angle neutron scattering

Zusammenfassung Um zu einem besseren Verständnis des Prozesses der Biomineralisation zu gelangen, muss das Zusammenwirken der verschiedenen Typen biologischer Makromoleküle, die am Keimbildungs- und Wachstumsprozess der Minerale beteiligt sind, berücksichtigt werden. In dieser Arbeit wird ein neues Modellsystem eingeführt, das aus einem SAM (self-assembled monolayer) mit verschiedenen Funktionalitäten und unterschiedlichen, gelösten Makromolekülen besteht. Es konnte gezeigt werden, dass die Kristallisation von Vaterit (CaCO3) sowie Strontianit (SrCO3) Nanodrähten der Präsenz von Polyacrylat in Kooperation mit einer COOH-funktionalisierten SAM-Oberfläche zugeschrieben werden kann. Die Kombination bestehend aus einer polaren SAM-Oberfläche und Polyacrylat fungiert als Grenzfläche für die Struktur dirigierende Kristallisation von Nanodraht-Kristallen. Weiter konnte gezeigt werden, dass die Phasenselektion von CaCO3 durch die kooperative Wechselwirkung zwischen einer SAM-Oberfläche und einem daran adsorbierten hb-Polyglycerol kontrolliert wird. Auch die Funktionalität einer SAM-Oberfläche in Gegenwart von Carboxymethyl-cellulose übt einen entscheidenden Einfluss auf die Phasenselektion des entstehenden Produktes aus. In der vorliegenden Arbeit wurden Untersuchungen an CaCO3 zur homogenen Keimbildung, zur Nukleation in Gegenwart eines Proteins sowie auf Kolloiden, die als Template fungieren, mittels Kleinwinkel-Neutronenstreuung durchgeführt. Die homogene Kristallisation in wässriger Lösung stellte sich als ein mehrstufiger Prozess heraus. In Gegenwart des Eiweißproteins Ovalbumin konnten drei Phasen identifiziert werden, darunter eine anfänglich vorhandene amorphe sowie zwei kristalline Phasen.

Magnetic properties of selected 3d- and 4f-systems on alpha-Al 2 O 3 substrates

In this work the growth and the magnetic properties of the transition metals molybdenum, niobium, and iron and of the highly-magnetostrictive C15 Laves phases of the RFe2 compounds (R: Rare earth metals: here Tb, Dy, and Tb{0.3}Dy{0.7} deposited on alpha-Al2O3 (sapphire) substrates are analyzed. Next to (11-20) (a-plane) oriented sapphire substrates mainly (10-10) (m-plane) oriented substrates were used. These show a pronounced facetting after high temperature annealing in air. Atomic force microscopy (AFM) measurements reveal a dependence of the height, width, and angle of the facets with the annealing temperature. The observed deviations of the facet angles with respect to the theoretical values of the sapphire (10-1-2) and (10-11) surfaces are explained by cross section high resolution transmission electron microscopy (HR-TEM) measurements. These show the plain formation of the (10-11) surface while the second, energy reduced (10-1-2) facet has a curved shape given by atomic steps of (10-1-2) layers and is formed completely solely at the facet ridges and valleys. Thin films of Mo and Nb, respectively, deposited by means of molecular beam epitaxy (MBE) reveal a non-twinned, (211)-oriented epitaxial growth as well on non-faceted as on faceted sapphire m-plane, as was shown by X-Ray and TEM evaluations. In the case of faceted sapphire the two bcc crystals overgrow the facets homogeneously. Here, the bcc (111) surface is nearly parallel to the sapphire (10-11) facet and the Mo/Nb (100) surface is nearly parallel to the sapphire (10-1-2) surface. (211)-oriented Nb templates on sapphire m-plane can be used for the non-twinned, (211)-oriented growth of RFe2 films by means of MBE. Again, the quality of the RFe2 films grown on faceted sapphire is almost equal to films on the non-faceted substrate. For comparison thin RFe2 films of the established (110) and (111) orientation were prepared. Magnetic and magnetoelastic measurements performed in a self designed setup reveal a high quality of the samples. No difference between samples with undulated and flat morphology can be observed. In addition to the preparation of covering, undulating thin films on faceted sapphire m-plane nanoscopic structures of Nb and Fe were prepared by shallow incidence MBE. The formation of the nanostructures can be explained by a shadowing of the atomic beam due to the facets in addition to de-wetting effects of the metals on the heated sapphire surface. Accordingly, the nanostructures form at the facet ridges and overgrow them. The morphology of the structures can be varied by deposition conditions as was shown for Fe. The shape of the structures vary from pearl-necklet strung spherical nanodots with a diameter of a few 10 nm to oval nanodots of a few 100 nm length to continuous nanowires. Magnetization measurements reveal uniaxial magnetic anisotropy with the easy axis of magnetization parallel to the facet ridges. The shape of the hysteresis is depending on the morphology of the structures. The magnetization reversal processes of the spherical and oval nanodots were simulated by micromagnetic modelling and can be explained by the formation of magnetic vortices.

Systematic studies of protein immobilization by surface plasmon field-enhanced fluorescence spectroscopy

The research interest of this study is to investigate surface immobilization strategies for proteins and other biomolecules by the surface plasmon field-enhanced fluorescence spectroscopy (SPFS) technique. The recrystallization features of the S-layer proteins and the possibility of combining the S-layer lattice arrays with other functional molecules make this protein a prime candidate for supramolecular architectures. The recrystallization behavior on gold or on the secondary cell wall polymer (SCWP) was recorded by SPR. The optical thicknesses and surface densities for different protein layers were calculated. In DNA hybridization tests performed in order to discriminate different mismatches, recombinant S-layer-streptavidin fusion protein matrices showed their potential for new microarrays. Moreover, SCWPs coated gold chips, covered with a controlled and oriented assembly of S-layer fusion proteins, represent an even more sensitive fluorescence testing platform. Additionally, S-layer fusion proteins as the matrix for LHCII immobilization strongly demonstrate superiority over routine approaches, proving the possibility of utilizing them as a new strategy for biomolecular coupling. In the study of the SPFS hCG immunoassay, the biophysical and immunological characteristics of this glycoprotein hormone were presented first. After the investigation of the effect of the biotin thiol dilution on the coupling efficiently, the interfacial binding model including the appropriate binary SAM structure and the versatile streptavidin-biotin interaction was chosen as the basic supramolecular architecture for the fabrication of a SPFS-based immunoassay. Next, the affinity characteristics between different antibodies and hCG were measured via an equilibrium binding analysis, which is the first example for the titration of such a high affinity interaction by SPFS. The results agree very well with the constants derived from the literature. Finally, a sandwich assay and a competitive assay were selected as templates for SPFS-based hCG detection, and an excellent LOD of 0.15 mIU/ml was attained via the “one step” sandwich method. Such high sensitivity not only fulfills clinical requirements, but is also better than most other biosensors. Fully understanding how LHCII complexes transfer the sunlight energy directionally and efficiently to the reaction center is potentially useful for constructing biomimetic devices as solar cells. After the introduction of the structural and the spectroscopic features of LHCII, different surface immobilization strategies of LHCII were summarized next. Among them the strategy based on the His-tag and the immobilized metal (ion) affinity chromatography (IMAC) technique were of great interest and resulted in different kinds of home-fabricated His-tag chelating chips. Their substantial protein coupling capacity, maintenance of high biological activity and a remarkably repeatable binding ability on the same chip after regeneration was demonstrated. Moreover, different parameters related to the stability of surface coupled reconstituted complexes, including sucrose, detergent, lipid, oligomerization, temperature and circulation rate, were evaluated in order to standardize the most effective immobilization conditions. In addition, partial lipid bilayers obtained from LHCII contained proteo-liposomes fusion on the surface were observed by the QCM technique. Finally, the inter-complex energy transfer between neighboring LHCIIs on a gold protected silver surface by excitation with a blue laser (λ = 473nm) was recorded for the first time, and the factors influencing the energy transfer efficiency were evaluated.

Thin functional conducting polymer films

In the present study, thin functional conducting polyaniline (PANI) films, either doped or undoped, patterned or unpatterned, were prepared by different approaches. The properties of the obtained PANI films were investigated in detail by a combination of electrochemistry with several other techniques, such as SPR, QCM, SPFS, diffraction, etc. The sensing applications (especially biosensing applications) of the prepared PANI films were explored. Firstly, the pure PANI films were prepared by the electropolymerisation method and their doping/dedoping properties in acidic conditions were investigated in detail by a combination of electrochemistry with SPR and QCM. Dielectric constants of PANI at different oxidation states were obtained quantitatively. The results obtained here laid a good foundation for the following investigations of PANI films in neutral pH conditions. Next, PANI multilayer films doped by a variety of materials were prepared by the layer-by-layer method in order to explore their biosensing applications, because of the loss of redox activity of pure PANI in neutral pH conditions. The dopants used include not only the traditionally used linear polyelectrolytes, but also, for the first tim, some other novel materials, like modified gold nanoparticles or modified carbon nanotubes. Our results showed that all the used dopants could form stable multilayer films with PANI. All the obtained PANI multilayer films showed good redox activity in a neutral pH environment, which makes them feasible for bioassays. We found that all the prepared PANI multilayer films can electrocatalyze the oxidation of NADH in neutral conditions at a low potential, although their catalytic efficiencies are different. Among them, PANI/carbon nanotube system showed the highest catalytic efficiency toward the oxidation of NADH, which makes it a good candidate as a NADH sensor. Besides, because some of the prepared PANI multilayer systems were end-terminated with –COOH groups (like PANI/Au nanoparticles system), which can be utilized to easily link biomolecules for biosensing applications. Here, we demonstrated, for the first time, to use the prepared PANI multilayer films for the DNA hybridisation detection. The detection event was monitored either by direct electrochemical method, or by enzyme-amplified electrochemical method, or by surface plasmon enhanced fluorescence spectroscopic method. All the methods can effectively differentiate non-complementary DNA from the complementary ones, even at the single-base mismatch level. It should also be noted that, our success in fabricating PANI multilayer films with modified Au nanoparticles or carbon nanotubes also offered another novel method for incorporating such novel materials into (conducting) polymers. Because of the unique electrochemical and optical properties of each component of the obtained PANI multilayer films, they should also find potential applications in many other fields such as microelectronics, or for electrochromic and photovoltaic devices. Finally, patterned PANI films were fabricated by the combination of several patterning techniques, such as the combination of electrocopolymerization with micromolding in capillaries (EP-MIMIC), the combination of microcontact printing with the layer-by-layer technique (µCP-LBL), and the polystyrene (PS) template induced electropolymerisation method. Using the obtained stripe-shaped PANI/PSS film, a redox-switchable polymer grating based on the surface-plasmon-enhanced mode was constructed and its application in the field of biosensing was explored. It was found that the diffraction efficiency (DE) of the grating was very sensitive to the applied potential (i.e. redox state of the film) as well as the pH environment of the dielectric medium. Moreover, the DE could also be effectively tuned by an electrocatalytic event, such as the electrocatalytic oxidation of NADH by the grating film. By using PS colloidal crystal assemblies as templates, well-ordered 3D interconnected macroporous PANI arrays (PANI inverse opals) were fabricated via electropolymerisation method. The quality of the obtained inverse opals was much higher than those reported by chemical synthesis method. By electrochemical method, the structures of the prepared inverse opals can be easily controlled. To explore the possible biosensing applications of PANI inverse opals, efforts were also done toward the fabrication of PANI composite inverse opals. By selecting proper dopants, high quality inverse opals of PANI composites were fabricated for the first time. And the obtained opaline films remained redox-active in neutral pH conditions, pointing to their possible applications for electrobioassays.

Nanostructuring by templated synthesis of nanowires and controlled crystallization of calcium phosphate on self-assembled monolayers

The idea was to obtain nanowires in a chemical laboratory under convenient and simple conditions by employing templates. Thus it was possible to produce nanochains by interlinking of gold colloids synthesized by the two-phase-method of M. Brust with by making use of vanadiumoxide nanotubes as template. The length of the resulting nanowires is varying between 1100 nm and 200 nm with a diameter of about 16 nm. Due to a flexible linker the obtained nanowires are not completely rigid. These unique structural features could make them interesting objects for structuring and assembling in the nanoscale range. Another way to produce gold nanowires was realized by a two-step surface metallization procedure, using type I collagen fibres as a template. Gold colloids were used to label the collagen fibres by direct electrostatic interaction, followed by growth steps to enhance the size of the adsorbed colloidal gold crystals, resulting in a complete metallization of the template surface. The length of the resulting gold nanowires reaches several micrometers, with a diameter ~ 100 to 120 nm. To gain a deeper insight into the process of biomineralization the cooperative effect of self-assembled monolayers as substrate and a soluble counterpart on the nucleation and crystal growth of calcium phosphate was studied by diffusion techniques with a pH switch as initiator. As soluble component Perlucin and Nacrein were used. Both are proteins originally extracted from marine organisms, the first one from the Abalone shell and the second one from oyster pearls. Both are supposed to facilitate the calcium carbonate formation in vivo. Studies with Perlucin revealed that this protein shows a clear cooperative effect at a very low concentration with a hydrophobic surface promoting the calcium phosphate precipitation resulting in a sponge like structure of hydroxyapatite. The Perlucin molecule is very flexible and is unfolded by adsorbing to the hydrophobic surface and uncovers its active side. Hydrophilic surfaces did not have a deeper impact. Studies with Nacrein as additive have shown that the protein stabilizes octacalcium phosphate at room temperature on carboxylic self-assembled monolayer and at 34 °C on all other employed surfaces by interaction with the mineral. On the hydroxyl-, alkyl-, and amin-terminated self-assembled monolayers at room temperature the octacalcium phosphate get transformed to hydroxyapatite. Main analytical techniques which are used in this work are transmission electron microscopy, high resolution scanning electron microscopy, surface plasmon resonance spectroscopy, atomic force microscopy, Raman micro-spectroscopy and quartz crystal microbalance.

Synthetic strategies of new molecular paramagnetic mechanically-interlocked complexes

Supramolecular chemistry is a multidisciplinary field which impinges on other disciplines, focusing on the systems made up of a discrete number of assembled molecular subunits. The forces responsible for the spatial organization are intermolecular reversible interactions. The supramolecular architectures I was interested in are Rotaxanes, mechanically-interlocked architectures consisting of a "dumbbell shaped molecule", threaded through a "macrocycle" where the stoppers at the end of the dumbbell prevent disassociation of components and catenanes, two or more interlocked macrocycles which cannot be separated without breaking the covalent bonds. The aim is to introduce one or more paramagnetic units to use the ESR spectroscopy to investigate complexation properties of these systems cause this technique works in the same time scale of supramolecular assemblies. Chapter 1 underlines the main concepts upon which supramolecular chemistry is based, clarifying the nature of supramolecular interactions and the principles of host-guest chemistry. In chapter 2 it is pointed out the use of ESR spectroscopy to investigate the properties of organic non-covalent assemblies in liquid solution by spin labels and spin probes. The chapter 3 deals with the synthesis of a new class of p-electron-deficient tetracationic cyclophane ring, carrying one or two paramagnetic side-arms based on 2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPO) moiety. In the chapter 4, the Huisgen 1,3-dipolar cycloaddition is exploited to synthesize rotaxanes having paramagnetic cyclodextrins as wheels. In the chapter 5, the catalysis of Huisgen’s cycloaddition by CB[6] is exploited to synthesize paramagnetic CB[6]-based [3]-rotaxanes. In the chapter 6 I reported the first preliminary studies of Actinoid series as a new class of templates in catenanes’ synthesis. Being f-block elements, so having the property of expanding the valence state, they constitute promising candidates as chemical templates offering the possibility to create a complex with coordination number beyond 6.

New platforms for optical biosensing

Physicochemical experimental techniques combined with the specificity of a biological recognition system have resulted in a variety of new analytical devices known as biosensors. Biosensors are under intensive development worldwide because they have many potential applications, e.g. in the fields of clinical diagnostics, food analysis, and environmental monitoring. Much effort is spent on the development of highly sensitive sensor platforms to study interactions on the molecular scale. In the first part, this thesis focuses on exploiting the biosensing application of nanoporous gold (NPG) membranes. NPG with randomly distributed nanopores (pore sizes less than 50 nm) will be discussed here. The NPG membrane shows unique plasmonic features, i.e. it supports both propagating and localized surface plasmon resonance modes (p SPR and l-SPR, respectively), both offering sensitive probing of the local refractive index variation on/in NPG. Surface refractive index sensors have an inherent advantage over fluorescence optical biosensors that require a chromophoric group or other luminescence label to transduce the binding event. In the second part, gold/silica composite inverse opals with macroporous structures were investigated with bio- or chemical sensing applications in mind. These samples combined the advantages of a larger available gold surface area with a regular and highly ordered grating structure. The signal of the plasmon was less noisy in these ordered substrate structures compared to the random pore structures of the NPG samples. In the third part of the thesis, surface plasmon resonance (SPR) spectroscopy was applied to probe the protein-protein interaction of the calcium binding protein centrin with the heterotrimeric G-protein transducin on a newly designed sensor platform. SPR spectroscopy was intended to elucidate how the binding of centrin to transducin is regulated towards understanding centrin functions in photoreceptor cells.

DNA block copolymers - synthesis, morphologies and applications

The last decades have witnessed significant and rapid progress in polymer chemistry and molecular biology. The invention of PCR and advances in automated solid phase synthesis of DNA have made this biological entity broadly available to all researchers across biological and chemical sciences. Thanks to the development of a variety of polymerization techniques, macromolecules can be synthesized with predetermined molecular weights and excellent structural control. In recent years these two exciting areas of research converged to generate a new type of nucleic acid hybrid material, consisting of oligodeoxynucleotides and organic polymers. By conjugating these two classes of materials, DNA block copolymers are generated exhibiting engineered material properties that cannot be realized with polymers or nucleic acids alone. Different synthetic strategies based on grafting onto routes in solution or on solid support were developed which afforded DNA block copolymers with hydrophilic, hydrophobic and thermoresponsive organic polymers in good yields. Beside the preparation of DNA block copolymers with a relative short DNA-segment, it was also demonstrated how these bioorganic polymers can be synthesized exhibiting large DNA blocks (>1000 bases) applying the polymerase chain reaction. Amphiphilic DNA block copolymers, which were synthesized fully automated in a DNA synthesizer, self-assemble into well-defined nanoparticles. Hybridization of spherical micelles with long DNA templates that encode several times the sequence of the micelle corona induced a transformation into rod-like micelles. The Watson-Crick motif aligned the hydrophobic polymer segments along the DNA double helix, which resulted in selective dimer formation. Even the length of the resulting nanostructures could be precisely adjusted by the number of nucleotides of the templates. In addition to changing the structural properties of DNA-b-PPO micelles, these materials were applied as 3D nanoscopic scaffolds for organic reactions. The DNA strands of the corona were organized by hydrophobic interactions of the organic polymer segments in such a fashion that several DNA-templated organic reactions proceeded in a sequence specific manner; either at the surface of the micelles or at the interface between the biological and the organic polymer blocks. The yields of reactions employing the micellar template were equivalent or better than existing template architectures. Aside from its physical properties and the morphologies achieved, an important requirement for a new biomaterial is its biocompatibility and interaction with living systems, i.e. human cells. The toxicity of the nanoparticles was analyzed by a cell proliferation assay. Motivated by the non-toxic nature of the amphiphilic DNA block copolymers, these nanoobjects were employed as drug delivery vehicles to target the anticancer drug to a tumor tissue. The micelles obtained from DNA block copolymers were easily functionalized with targeting units by hybridization. This facile route allowed studying the effect of the amount of targeting units on the targeting efficacy. By varying the site of functionalization, i.e. 5’ or 3’, the outcome of having the targeting unit at the periphery of the micelle or in the core of the micelle was studied. Additionally, these micelles were loaded with an anticancer drug, doxorubicin, and then applied to tumor cells. The viability of the cells was calculated in the presence and absence of targeting unit. It was demonstrated that the tumor cells bearing folate receptors showed a high mortality when the targeting unit was attached to the nanocarrier.

Cell-free cryopreserved arterial allografts from multiorgan donors: a new strategy to fabricate artificial blood vessels suited for peripheral vascular surgery

Critical lower limb ischemia is a severe disease. A common approach is infrainguinal bypass. Synthetic vascular prosthesis, are good conduits in high-flow low-resistance conditions but have difficulty in their performance as small diameter vessel grafts. A new approach is the use of native decellularized vascular tissues. Cell-free vessels are expected to have improved biocompatibility when compared to synthetic and are optimal natural 3D matrix templates for driving stem cell growth and tissue assembly in vivo. Decellularization of tissues represent a promising field for regenerative medicine, with the aim to develop a methodology to obtain small-diameter allografts to be used as a natural scaffold suited for in vivo cell growth and pseudo-tissue assembly, eliminating failure caused from immune response activation. Material and methods. Umbilical cord-derived mesenchymal cells isolated from human umbilical cord tissue were expanded in advanced DMEM. Immunofluorescence and molecular characterization revealed a stem cell profile. A non-enzymatic protocol, that associate hypotonic shock and low-concentration ionic detergent, was used to decellularize vessel segments. Cells were seeded cell-free scaffolds using a compound of fibrin and thrombin and incubated in DMEM, after 4 days of static culture they were placed for 2 weeks in a flow-bioreactor, mimicking the cardiovascular pulsatile flow. After dynamic culture, samples were processed for histological, biochemical and ultrastructural analysis. Discussion. Histology showed that the dynamic culture cells initiate to penetrate the extracellular matrix scaffold and to produce components of the ECM, as collagen fibres. Sirius Red staining showed layers of immature collagen type III and ultrastructural analysis revealed 30 nm thick collagen fibres, presumably corresponding to the immature collagen. These data confirm the ability of cord-derived cells to adhere and penetrate a natural decellularized tissue and to start to assembly into new tissue. This achievement makes natural 3D matrix templates prospectively valuable candidates for clinical bypass procedures

Surface-plasmon optical and electrochemical characterization of biofunctional surface architectures

The development and characterization of biomolecule sensor formats based on the optical technique Surface Plasmon Resonance (SPR) Spectroscopy and electrochemical methods were investigated. The study can be divided into two parts of different scope. In the first part new novel detection schemes for labeled targets were developed on the basis of the investigations in Surface-plamon Field Enhanced Spectroscopy (SPFS). The first one is SPR fluorescence imaging formats, Surface-plamon Field Enhanced Fluorescence Microscopy (SPFM). Patterned self assembled monolayers (SAMs) were prepared and used to direct the spatial distribution of biomolecules immobilized on surfaces. Here the patterned monolayers would serve as molecular templates to secure different biomolecules to known locations on a surface. The binding processed of labeled target biomolecules from solution to sensor surface were visually and kinetically recorded by the fluorescence microscope, in which fluorescence was excited by the evanescent field of propagating plasmon surface polaritons. The second format which also originates from SPFS technique, Surface-plamon Field Enhanced Fluorescence Spectrometry (SPFSm), concerns the coupling of a fluorometry to normal SPR setup. A spectrograph mounted in place of photomultiplier or microscope can provide the information of fluorescence spectrum as well as fluorescence intensity. This study also firstly demonstrated the analytical combination of surface plasmon enhanced fluorescence detection with analyte tagged by semiconducting nano- crystals (QDs). Electrochemically addressable fabrication of DNA biosensor arrays in aqueous environment was also developed. An electrochemical method was introduced for the directed in-situ assembly of various specific oligonucleotide catcher probes onto different sensing elements of a multi-electrode array in the aqueous environment of a flow cell. Surface plasmon microscopy (SPM) is utilized for the on-line recording of the various functionalization steps. Hybridization reactions between targets from solution to the different surface-bound complementary probes are monitored by surface-plasmon field-enhanced fluorescence microscopy (SPFM) using targets that are either labeled with organic dyes or with semiconducting quantum dots for color-multiplexing. This study provides a new approach for the fabrication of (small) DNA arrays and the recording and quantitative evaluation of parallel hybridization reactions. In the second part of this work, the ideas of combining the SP optical and electrochemical characterization were extended to tethered bilayer lipid membrane (tBLM) format. Tethered bilayer lipid membranes provide a versatile model platform for the study of many membrane related processes. The thiolipids were firstly self-assembled on ultraflat gold substrates. Fusion of the monolayers with small unilamellar vesicles (SUVs) formed the distal layer and the membranes thus obtained have the sealing properties comparable to those of natural membranes. The fusion could be monitored optically by SPR as an increase in reflectivity (thickness) upon formation of the outer leaflet of the bilayer. With EIS, a drop in capacitance and a steady increase in resistance could be observed leading to a tightly sealing membrane with low leakage currents. The assembly of tBLMs and the subsequent incorporation of membrane proteins were investigated with respect to their potential use as a biosensing system. In the case of valinomycin the potassium transport mediated by the ion carrier could be shown by a decrease in resistance upon increasing potassium concentration. Potential mediation of membrane pores could be shown for the ion channel forming peptide alamethicin (Alm). It was shown that at high positive dc bias (cis negative) Alm channels stay at relatively low conductance levels and show higher permeability to potassium than to tetramethylammonium. The addition of inhibitor amiloride can partially block the Alm channels and results in increase of membrane resistance. tBLMs are robust and versatile model membrane architectures that can mimic certain properties of biological membranes. tBLMs with incorporated lipopolysaccharide (LPS) and lipid A mimicking bacteria membranes were used to probe the interactions of antibodies against LPS and to investigate the binding and incorporation of the small antimicrobial peptide V4. The influence of membrane composition and charge on the behavior of V4 was also probed. This study displays the possibility of using tBLM platform to record and valuate the efficiency or potency of numerous synthesized antimicrobial peptides as potential drug candidates.

Nanoscale effects and applications of self-organized nanostructured thin films

A nanostructured thin film is a thin material layer, usually supported by a (solid) substrate, which possesses subdomains with characteristic nanoscale dimensions (10 ~ 100 nm) that are differentiated by their material properties. Such films have captured vast research interest because the dimensions and the morphology of the nanostructure introduce new possibilities to manipulating chemical and physical properties not found in bulk materials. Block copolymer (BCP) self-assembly, and anodization to form nanoporous anodic aluminium oxide (AAO), are two different methods for generating nanostructures by self-organization. Using poly(styrene-block-methyl methacrylate) (PS-b-PMMA) nanopatterned thin films, it is demonstrated that these polymer nanopatterns can be used to study the influence of nanoscale features on protein-surface interactions. Moreover, a method for the directed assembly of adsorbed protein nanoarrays, based on the nanoscale juxtaposition of the BCP surface domains, is also demonstrated. Studies on protein-nanopattern interactions may inform the design of biomaterials, biosensors, and relevant cell-surface experiments that make use of nanoscale structures. In addition, PS-b-PMMA and AAO thin films are also demonstrated for use as optical waveguides at visible wavelengths. Due to the sub-wavelength nature of the nanostructures, scattering losses are minimized, and the optical response is amenable to analysis with effective medium theory (EMT). Optical waveguide measurements and EMT analysis of the films’ optical anisotropy enabled the in situ characterization of the PS-b-PMMA nanostructure, and a variety of surface processes within the nanoporous AAO involving (bio)macromolecules at high sensitivity.