Synthesis, multiscale-multiphase characterization and applications of thiophene-based biohybrids

Biohybrid derivatives of π-conjugated materials are emerging as powerful tools to study biological events through the (opto)electronic variations of the π-conjugated moieties, as well as to direct and govern the self-assembly properties of the organic materials through the organization principles of the bio component. So far, very few examples of thiophene-based biohybrids have been reported. The aim of this Ph. D thesis has been the development of oligothiophene-oligonucleotide hybrid derivatives as tools, on one side, to detect DNA hybridisation events and, on the other, as model compounds to investigate thiophene-nucleobase interactions in the solid state. To obtain oligothiophene bioconjugates with the required high level of purity, we first developed new synthetic ecofriendly protocols for the synthesis of thiophene oligomers. Our innovative heterogeneous Suzuki coupling methodology, carried out in EtOH/water or isopropanol under microwave irradiation, allowed us to obtain alkyl substituted oligothiophenes and thiophene based co-oligomers in high yields and very short reaction times, free from residual metals and with improved film forming properties. These methodologies were subsequently applied in the synthesis of oligothiophene-oligonucleotide conjugates. Oligothiophene-5-labeled deoxyuridines were synthesized and incorporated into 19-meric oligonucletide sequences. We showed that the oligothiophene-labeled oligonucletide sequences obtained can be used as probes to detect a single nucleotide polymorphism (SNP) in complementary DNA target sequences. In fact, all the probes showed marked variations in emission intensity upon hybridization with a complementary target sequence. The observed variations in emitted light were comparable or even superior to those reported in similar studies, showing that the biohybrids can potentially be useful to develop biosensors for the detection of DNA mismatches. Finally, water-soluble, photoluminescent and electroactive dinucleotide-hybrid derivatives of quaterthiophene and quinquethiophene were synthesized. By means of a combination of spectroscopy and microscopy techniques, electrical characterizations, microfluidic measurements and theoretical calculations, we were able to demonstrate that the self-assembly modalities of the biohybrids in thin films are driven by the interplay of intra and intermolecular interactions in which the π-stacking between the oligothiophene and nucleotide bases plays a major role.

Applications of High Speed Configurable Logic Devices in Modern Particle Physics Experiments

Several activities were conducted during my PhD activity. For the NEMO experiment a collaboration between the INFN/University groups of Catania and Bologna led to the development and production of a mixed signal acquisition board for the Nemo Km3 telescope. The research concerned the feasibility study for a different acquisition technique quite far from that adopted in the NEMO Phase 1 telescope. The DAQ board that we realized exploits the LIRA06 front-end chip for the analog acquisition of anodic an dynodic sources of a PMT (Photo-Multiplier Tube). The low-power analog acquisition allows to sample contemporaneously multiple channels of the PMT at different gain factors in order to increase the signal response linearity over a wider dynamic range. Also the auto triggering and self-event-classification features help to improve the acquisition performance and the knowledge on the neutrino event. A fully functional interface towards the first level data concentrator, the Floor Control Module, has been integrated as well on the board, and a specific firmware has been realized to comply with the present communication protocols. This stage of the project foresees the use of an FPGA, a high speed configurable device, to provide the board with a flexible digital logic control core. After the validation of the whole front-end architecture this feature would be probably integrated in a common mixed-signal ASIC (Application Specific Integrated Circuit). The volatile nature of the configuration memory of the FPGA implied the integration of a flash ISP (In System Programming) memory and a smart architecture for a safe remote reconfiguration of it. All the integrated features of the board have been tested. At the Catania laboratory the behavior of the LIRA chip has been investigated in the digital environment of the DAQ board and we succeeded in driving the acquisition with the FPGA. The PMT pulses generated with an arbitrary waveform generator were correctly triggered and acquired by the analog chip, and successively they were digitized by the on board ADC under the supervision of the FPGA. For the communication towards the data concentrator a test bench has been realized in Bologna where, thanks to a lending of the Roma University and INFN, a full readout chain equivalent to that present in the NEMO phase-1 was installed. These tests showed a good behavior of the digital electronic that was able to receive and to execute command imparted by the PC console and to answer back with a reply. The remotely configurable logic behaved well too and demonstrated, at least in principle, the validity of this technique. A new prototype board is now under development at the Catania laboratory as an evolution of the one described above. This board is going to be deployed within the NEMO Phase-2 tower in one of its floors dedicated to new front-end proposals. This board will integrate a new analog acquisition chip called SAS (Smart Auto-triggering Sampler) introducing thus a new analog front-end but inheriting most of the digital logic present in the current DAQ board discussed in this thesis. For what concern the activity on high-resolution vertex detectors, I worked within the SLIM5 collaboration for the characterization of a MAPS (Monolithic Active Pixel Sensor) device called APSEL-4D. The mentioned chip is a matrix of 4096 active pixel sensors with deep N-well implantations meant for charge collection and to shield the analog electronics from digital noise. The chip integrates the full-custom sensors matrix and the sparsifification/readout logic realized with standard-cells in STM CMOS technology 130 nm. For the chip characterization a test-beam has been set up on the 12 GeV PS (Proton Synchrotron) line facility at CERN of Geneva (CH). The collaboration prepared a silicon strip telescope and a DAQ system (hardware and software) for data acquisition and control of the telescope that allowed to store about 90 million events in 7 equivalent days of live-time of the beam. My activities concerned basically the realization of a firmware interface towards and from the MAPS chip in order to integrate it on the general DAQ system. Thereafter I worked on the DAQ software to implement on it a proper Slow Control interface of the APSEL4D. Several APSEL4D chips with different thinning have been tested during the test beam. Those with 100 and 300 um presented an overall efficiency of about 90% imparting a threshold of 450 electrons. The test-beam allowed to estimate also the resolution of the pixel sensor providing good results consistent with the pitch/sqrt(12) formula. The MAPS intrinsic resolution has been extracted from the width of the residual plot taking into account the multiple scattering effect.

Noisy Oncology: applications of bounded noise transitions in modelling tumor growth

I tumori macroscopici e microscopici, dopo la loro prima fase di crescita, sono composti da un numero medio elevato di cellule. Così, in assenza di perturbazioni esterne, la loro crescita e i punti di equilibrio possono essere descritti da equazioni differenziali. Tuttavia, il tumore interagisce fortemente col macroambiente che lo circonda e di conseguenza una descrizione del tutto deterministica risulta a volte inappropriata. In questo caso si può considerare l'interazione con fluttuazioni statistiche, causate da disturbi esterni, utilizzando le equazioni differenziali stocastiche (SDE). Questo è vero in modo particolare quando si cerca di modellizzare tumori altamente immunogenici che interagiscono con il sistema immunitario, in quanto la complessità di questa interazione risulta in fenomeni di multistabilità. Così, il rumore può provocare disturbi e indurre transizioni di stato (Noise-Induced-Transitions). E' importante notare che una NIT può avere implicazioni profonde sulla vita di un paziente, dal momento che una transizione da uno stato di equilibrio piccolo, nelle dimensioni del tumore, ad uno stato di equilibrio macroscopico, nella maggior parte dei casi significa il passaggio dalla vita alla morte. Generalmente l'approccio standard è quello di modellizzare le fluttuazioni stocastiche dei parametri per mezzo di rumore gaussiano bianco o colorato. In alcuni casi però questa procedura è altamente inadeguata, a causa della illimitatezza intrinseca dei rumori gaussiani che può portare a gravi incongruenze biologiche: pertanto devono essere utilizzati dei rumori "limitati", che, tuttavia, sono molto meno studiati di quelli gaussiani. Inoltre, l'insorgenza di NIT dipende dal tipo di rumore scelto, che rivela un nuovo livello di complessità in biologia. Lo scopo di questa tesi è quello di studiare le applicazioni di due tipi diversi di "rumori limitati" nelle transizioni indotte in due casi: interazione tra tumore e sistema immunitario e chemioterapia dei tumori. Nel primo caso, abbiamo anche introdotto un nuovo modello matematico di terapia, che estende, in modo nuovo, il noto modello di Norton-Simon.

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

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

Extraterrestrial and terrestrial outdoor applications of Mössbauer spectroscopy

„Extraterrestrische und terrestrische Anwendungen eines miniaturisierten Mössbauer-Spektrometers“ Die vorliegende Arbeit befasst sich mit Anwendungen eines miniaturisierten Mössbauer- Spektrometers (MIMOS II), dessen Entwicklung in den frühen neunziger Jahren am Institut für Kernphysik der Technischen Universität Darmstadt unter Professor Egbert Kankeleit und seinen Mitarbeitern begann. Seit 1998 sind die Entwicklungsarbeiten im Arbeitskreis von Prof. Gütlich am Institut für Anorganische und Analytische Chemie der Johannes Gutenberg- Universität Mainz von Dr. Göstar Klingelhöfer und Mitarbeitern fortgesetzt worden. Vorrangiges Ziel war dabei der geplante Einsatz des Spektrometers zu mineralogischen Untersuchungen im Weltall. Entsprechend ist das Projekt mit erheblichen finanziellen Mitteln des Forschungsinstituts der Deutschen Luft- und Raumfahrt (DLR) in Bonn unterstützt worden. Bei den beiden Missionen, die im Jahre 2003 von der NASA zum Mars gesandt wurden und im Januar dieses Jahres die beiden „Mars Exploration Rover“ (MER) "Spirit" und "Opportunity" erfolgreich auf der Marsoberfläche abgesetzt haben, ist jeweils ein MIMOS II-Gerät zur Charakterisierung eisenhaltiger Minerale und Böden während der laufenden Mission im Einsatz. Einige Ergebnisse von MIMOS II an Gestein und Böden der Marsoberfläche werden in der vorliegenden Arbeit präsentiert und diskutiert. Diese Ergebnisse wurden vom MIMOS II-Consortium unter Führung von Dr. Göstar Klingelhöfer, mit Unterstützung des Ingenieurs- und Wissenschaftsteams von MER am Jet Propulsion Laboratory in Kalifornien, erlangt. Erste Spektren, die von Proben im Gusev-Krater (Landestelle von „Spirit“) aufgenommen wurden und in dieser Arbeit vorgestellt werden, weisen auf das Vorkommen von forsteritischem Olivin, Pyroxen, Magnetit hin; daneben zeigt sich ein von Eisen(III) herrührendes Quadrupoldublett, das (noch) nicht eindeutig zugeordnet werden konnte. Aus den gewonnenen Daten wurde geschlossen, dass physikalische Verwitterung der vorherrschende Veränderungsprozess in den Ebenen des Gusev-Kraters ist. Um die Fähigkeiten von MIMOS II in der Charakteriserung extraterrestrischen Materials vor dem Start zum Mars zu demonstrieren, wurde eine Auswahl von chondritischen, Eisenund Marsmeteoriten gemessen. Ein Datenanalysepaket, basierend auf künstlichen neuronalen Netzwerken, genetischen Algorithmen und "fuzzy" Logik, wurde erstellt, erfolgreich getestet und während der Echtzeit-Operation der MER benutzt. Eine Datenbasis von Mössbauer-Parametern und Referenzen von veröffentlichten Studien über den Temperaturbereich des Mars wurde zusammengestellt. Die Werkzeuge zur Datenanalyse eröffnen neue Einsatzmöglichkeiten des miniaturisierten Mössbauer-Spektrometers in vielen Bereichen ausserhalb des Physikllabors. Einige davon werden in dieser Arbeit vorgestellt, wie z.B.die Pigmentcharakterisierung, die Echtheit archäologischer Artefakte oder in-situ Luftverschmutzungsmessungen. Datum: 20.07.2004 1. Betreuer: Professor Dr. P. Gütlich Paulo A. de Souza Jr. GAFEP/GETEP Departamento de Pelotização - DIPE Companhia Vale do Rio Doce - CVRD Tel.: (27) 3333-4609 - Carrier (835)

Bioanalytical applications of multicolour bioluminescence imaging: new tools for drug discovery and development

The subject of this thesis is multicolour bioluminescence analysis and how it can provide new tools for drug discovery and development.The mechanism of color tuning in bioluminescent reactions is not fully understood yet but it is object of intense research and several hypothesis have been generated. In the past decade key residues of the active site of the enzyme or in the surface surrounding the active site have been identified as responsible of different color emission. Anyway since bioluminescence reaction is strictly dependent from the interaction between the enzyme and its substrate D-luciferin, modification of the substrate can lead to a different emission spectrum too. In the recent years firefly luciferase and other luciferases underwent mutagenesis in order to obtain mutants with different emission characteristics. Thanks to these new discoveries in the bioluminescence field multicolour luciferases can be nowadays employed in bioanalysis for assay developments and imaging purposes. The use of multicolor bioluminescent enzymes expanded the potential of a range of application in vitro and in vivo. Multiple analysis and more information can be obtained from the same analytical session saving cost and time. This thesis focuses on several application of multicolour bioluminescence for high-throughput screening and in vivo imaging. Multicolor luciferases can be employed as new tools for drug discovery and developments and some examples are provided in the different chapters. New red codon optimized luciferase have been demonstrated to be improved tools for bioluminescence imaging in small animal and the possibility to combine red and green luciferases for BLI has been achieved even if some aspects of the methodology remain challenging and need further improvement. In vivo Bioluminescence imaging has known a rapid progress since its first application no more than 15 years ago. It is becoming an indispensable tool in pharmacological research. At the same time the development of more sensitive and implemented microscopes and low-light imager for a better visualization and quantification of multicolor signals would boost the research and the discoveries in life sciences in general and in drug discovery and development in particular.

Applications of RFID in the pharmaceutical supply chain

L’obiettivo di questa tesi è principalmente quello di mostrare le possibili applicazioni della tecnologia RFID (Radio Frequency Identification) all’interno della supply chain farmaceutica, cercando di comprendere il campo di applicazione di questa tecnologia in un’industria così altamente regolata e complessa come quella farmaceutica. La tesi è organizzata in tre sezioni; nel primo capitolo si trattano i principi alla base della tecnologia RFID e l’attuale stato dell’arte nella standardizzazione della banda di frequenza utilizzata e nell’hardware. In questa sezione sono poi mostrate le principali applicazioni e nella parte finale i problemi affrontati da un’azienda nell’applicare l’RFID al proprio business. Il secondo capitolo descrive le parti coinvolte nell’industria farmaceutica, dal produttore al consumatore finale, poi esamina le caratteristiche essenziali della supply chain farmaceutica e gli aspetti chiave e le criticità da affrontare in questo campo per essere efficiente e per consegnare il prodotto al cliente in maniera sicura e consistente. Infine nell’ultima sezione i due argomenti centrali sono fusi assieme, cercando di esaminare come la tecnologia RFID sia in grado di risolvere i problemi affrontati da tale industria. Il lavoro non vuole mostrare la tecnologia RFID come una panacea di tutte le problematiche presentate in questa industria, ma vuole cercare di colmare il gap presente in letteratura riguardo le possibili applicazioni di questa tecnologia nell’industria specificata.

Chemical Production and Microelectronic Applications of Graphene and Nano-Graphene Derivatives

Graphene and graphenic derivatives have rapidly emerged as an extremely promising system for electronic, optical, thermal, and electromechanical applications. Several approaches have been developed to produce these materials (i.e. scotch tape, CVD, chemical and solvent exfoliation). In this work we report a chemical approach to produce graphene by reducing graphene oxide (GO) via thermal or electrical methods. A morphological and electrical characterization of these systems has been performed using different techniques such as SPM, SEM, TEM, Raman and XPS. Moreover, we studied the interaction between graphene derivates and organic molecules focusing on the following aspects: - improvement of optical contrast of graphene on different substrates for rapid monolayer identification1 - supramolecular interaction with organic molecules (i.e. thiophene, pyrene etc.)4 - covalent functionalization with optically active molecules2 - preparation and characterization of organic/graphene Field Effect Transistors3-5 Graphene chemistry can potentially allow seamless integration of graphene technology in organic electronics devices to improve device performance and develop new applications for graphene-based materials. [1] E. Treossi, M. Melucci, A. Liscio, M. Gazzano, P. Samorì, and V. Palermo, J. Am. Chem. Soc., 2009, 131, 15576. [2] M. Melucci, E. Treossi, L. Ortolani, G. Giambastiani, V. Morandi, P. Klar, C. Casiraghi, P. Samorì, and V. Palermo, J. Mater. Chem., 2010, 20, 9052. [3] J.M. Mativetsky, E. Treossi, E. Orgiu, M. Melucci, G.P. Veronese, P. Samorì, and V. Palermo, J. Am. Chem. Soc., 2010, 132, 14130. [4] A. Liscio, G.P. Veronese, E. Treossi, F. Suriano, F. Rossella, V. Bellani, R. Rizzoli, P. Samorì and V. Palermo, J. Mater. Chem., 2011, 21, 2924. [5] J.M. Mativetsky, A. Liscio, E. Treossi, E. Orgiu, A. Zanelli, P. Samorì , V. Palermo, J. Am. Chem. Soc., 2011, 133, 14320

Applications of remote sensing and geographic information systems in geomorphological studies: Safaga - El Quseir area, Red Sea coast, Egypt as an example

In den letzten drei Jahrzehnten sind Fernerkundung und GIS in den Geowissenschaften zunehmend wichtiger geworden, um die konventionellen Methoden von Datensammlung und zur Herstellung von Landkarten zu verbessern. Die vorliegende Arbeit befasst sich mit der Anwendung von Fernerkundung und geographischen Informationssystemen (GIS) für geomorphologische Untersuchungen. Durch die Kombination beider Techniken ist es vor allem möglich geworden, geomorphologische Formen im Überblick und dennoch detailliert zu erfassen. Als Grundlagen werden in dieser Arbeit topographische und geologische Karten, Satellitenbilder und Klimadaten benutzt. Die Arbeit besteht aus 6 Kapiteln. Das erste Kapitel gibt einen allgemeinen Überblick über den Untersuchungsraum. Dieser umfasst folgende morphologische Einheiten, klimatischen Verhältnisse, insbesondere die Ariditätsindizes der Küsten- und Gebirgslandschaft sowie das Siedlungsmuster beschrieben. Kapitel 2 befasst sich mit der regionalen Geologie und Stratigraphie des Untersuchungsraumes. Es wird versucht, die Hauptformationen mit Hilfe von ETM-Satellitenbildern zu identifizieren. Angewandt werden hierzu folgende Methoden: Colour Band Composite, Image Rationing und die sog. überwachte Klassifikation. Kapitel 3 enthält eine Beschreibung der strukturell bedingten Oberflächenformen, um die Wechselwirkung zwischen Tektonik und geomorphologischen Prozessen aufzuklären. Es geht es um die vielfältigen Methoden, zum Beispiel das sog. Image Processing, um die im Gebirgskörper vorhandenen Lineamente einwandfrei zu deuten. Spezielle Filtermethoden werden angewandt, um die wichtigsten Lineamente zu kartieren. Kapitel 4 stellt den Versuch dar, mit Hilfe von aufbereiteten SRTM-Satellitenbildern eine automatisierte Erfassung des Gewässernetzes. Es wird ausführlich diskutiert, inwieweit bei diesen Arbeitsschritten die Qualität kleinmaßstäbiger SRTM-Satellitenbilder mit großmaßstäbigen topographischen Karten vergleichbar ist. Weiterhin werden hydrologische Parameter über eine qualitative und quantitative Analyse des Abflussregimes einzelner Wadis erfasst. Der Ursprung von Entwässerungssystemen wird auf der Basis geomorphologischer und geologischer Befunde interpretiert. Kapitel 5 befasst sich mit der Abschätzung der Gefahr episodischer Wadifluten. Die Wahrscheinlichkeit ihres jährlichen Auftretens bzw. des Auftretens starker Fluten im Abstand mehrerer Jahre wird in einer historischen Betrachtung bis 1921 zurückverfolgt. Die Bedeutung von Regentiefs, die sich über dem Roten Meer entwickeln, und die für eine Abflussbildung in Frage kommen, wird mit Hilfe der IDW-Methode (Inverse Distance Weighted) untersucht. Betrachtet werden außerdem weitere, regenbringende Wetterlagen mit Hilfe von Meteosat Infrarotbildern. Genauer betrachtet wird die Periode 1990-1997, in der kräftige, Wadifluten auslösende Regenfälle auftraten. Flutereignisse und Fluthöhe werden anhand von hydrographischen Daten (Pegelmessungen) ermittelt. Auch die Landnutzung und Siedlungsstruktur im Einzugsgebiet eines Wadis wird berücksichtigt. In Kapitel 6 geht es um die unterschiedlichen Küstenformen auf der Westseite des Roten Meeres zum Beispiel die Erosionsformen, Aufbauformen, untergetauchte Formen. Im abschließenden Teil geht es um die Stratigraphie und zeitliche Zuordnung von submarinen Terrassen auf Korallenriffen sowie den Vergleich mit anderen solcher Terrassen an der ägyptischen Rotmeerküste westlich und östlich der Sinai-Halbinsel.

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.

Applications of infrared thermography in the food industry

In the last 20-30 years, the implementation of new technologies from the research centres to the food industry process was very fast. The infrared thermography is a tool used in many fields, including agriculture and food science technology, because of it's important qualities like non-destructive method, it is fast, it is accurate, it is repeatable and economical. Almost all the industrial food processors have to use the thermal process to obtain an optimal product respecting the quality and safety standards. The control of temperature of food products during the production, transportation, storage and sales is an essential process in the food industry network. This tool can minimize the human error during the control of heat operation, and reduce the costs with personal. In this thesis the application of infrared thermography (IRT) was studies for different products that need a thermal process during the food processing. The background of thermography was presented, and also some of its applications in food industry, with the benefits and limits of applicability. The measurement of the temperature of the egg shell during the heat treatment in natural convection and with hot-air treatment was compared with the calculated temperatures obtained by a simplified finite element model made in the past. The complete process shown a good results between calculated and observed temperatures and we can say that this technique can be useful to control the heat treatments for decontamination of egg using the infrared thermography. Other important application of IRT was to determine the evolution of emissivity of potato raw during the freezing process and the control non-destructive control of this process. We can conclude that the IRT can represent a real option for the control of thermal process from the food industry, but more researches on various products are necessary.

The Dynamics of Passive Torsional Fatigue Test Rigs: Innovative Applications of Universal Joints

The dynamics of a passive back-to-back test rig have been characterised, leading to a multi-coordinate approach for the analysis of arbitrary test configurations. Universal joints have been introduced into a typical pre-loaded back-to-back system in order to produce an oscillating torsional moment in a test specimen. Two different arrangements have been investigated using a frequency-based sub-structuring approach: the receptance method. A numerical model has been developed in accordance with this theory, allowing interconnection of systems with two-coordinates and closed multi-loop schemes. The model calculates the receptance functions and modal and deflected shapes of a general system. Closed form expressions of the following individual elements have been developed: a servomotor, damped continuous shaft and a universal joint. Numerical results for specific cases have been compared with published data in literature and experimental measurements undertaken in the present work. Due to the complexity of the universal joint and its oscillating dynamic effects, a more detailed analysis of this component has been developed. Two models have been presented. The first represents the joint as two inertias connected by a massless cross-piece. The second, derived by the dynamic analysis of a spherical four-link mechanism, considers the contribution of the floating element and its gyroscopic effects. An investigation into non-linear behaviour has led to a time domain model that utilises the Runge-Kutta fourth order method for resolution of the dynamic equations. It has been demonstrated that the torsional receptances of a universal joint, derived using the simple model, result in representation of the joint as an equivalent variable inertia. In order to verify the model, a test rig has been built and experimental validation undertaken. The variable inertia of a universal joint has lead to a novel application of the component as a passive device for the balancing of inertia variations in slider-crank mechanisms.

New biosensor applications of surface plasmon and hydrogel optical waveguide spectroscopy

Rapid and sensitive detection of chemical and biological analytes becomes increasingly important in areas such as medical diagnostics, food control and environmental monitoring. Optical biosensors based on surface plasmon resonance (SPR) and optical waveguide spectroscopy have been extensively pushed forward in these fields. In this study, we combine SPR, surface plasmon-enhanced fluorescence spectroscopy (SPFS) and optical waveguide spectroscopy with hydrogel thin film for highly sensitive detection of molecular analytes.rnrnA novel biosensor based on SPFS which was advanced through the excitation of long range surface plasmons (LRSPs) is reported in this study. LRSPs are special surface plasmon waves propagating along thin metal films with orders of magnitude higher electromagnetic field intensity and lower damping than conventional SPs. Therefore, their excitation on the sensor surface provides further increased fluorescence signal. An inhibition immunoassay based on LRSP-enhanced fluorescence spectroscopy (LRSP-FS) was developed for the detection of aflatoxin M1 (AFM1) in milk. The biosensor allowed for the detection of AFM1 in milk at concentrations as low as 0.6 pg mL-1, which is about two orders of magnitude lower than the maximum AFM1 residue level in milk stipulated by the European Commission legislation.rnrnIn addition, LRSPs probe the medium adjacent to the metallic surface with more extended evanescent field than regular SPs. Therefore, three-dimensional binding matrices with up to micrometer thickness have been proposed for the immobilization of biomolecular recognition elements with large surface density that allows to exploit the whole evanescent field of LRSP. A photocrosslinkable carboxymethyl dextran (PCDM) hydrogel thin film is used as a binding matrix, and it is applied for the detection of free prostate specific antigen (f-PSA) based on the LRSP-FS and sandwich immunoassay. We show that this approach allows for the detection of f-PSA at low femto-molar range, which is approximately four orders of magnitude lower than that for direct detection of f-PSA based on the monitoring of binding-induced refractive index changes.rnrnHowever, a three dimensional hydrogel binding matrix with micrometer thickness can also serve as an optical waveguide. Based on the measurement of binding-induced refractive index changes, a hydrogel optical waveguide spectroscopy (HOWS) is reported for a label-free biosensor. This biosensor is implemented by using a SPR optical setup in which a carboxylated poly(N-isoproprylacrylamide) (PNIPAAm) hydrogel film is attached on a metallic surface and modified by protein catcher molecules. Compared to regular SPR biosensor with thiol self-assembled monolayer (SAM), HOWS provides an order of magnitude improved resolution in the refractive index measurements and enlarged binding capacity owing to its low damping and large swelling ratio, respectively. A model immunoassay experiment revealed that HOWS allowed detection of IgG molecules with a 10 pM limit of detection (LOD) that was five-fold lower than that achieved for SPR with thiol SAM. For the high capacity hydrogel matrix, the affinity binding was mass transport limited.rnrnThe mass transport of target molecules to the sensor surface can play as critical a role as the chemical reaction itself. In order to overcome the diffusion-limited mass transfer, magnetic iron oxide nanoparticles were employed. The magnetic nanoparticles (MNPs) can serve both as labels providing enhancement of the refractive index changes, and “vehicles” for rapidly delivering the analytes from sample solution to an SPR sensor surface with a gradient magnetic field. A model sandwich assay for the detection of β human chorionic gonadotropin (βhCG) has been utilized on a gold sensor surface with metallic diffraction grating structure supporting the excitation of SPs. Various detection formats including a) direct detection, b) sandwich assay, c) MNPs immunoassay without and d) with applied magnetic field were compared. The results show that the highly-sensitive MNPs immunoassay improves the LOD on the detection of βhCG by a factor of 5 orders of magnitude with respect to the direct detection.rn