Dissertations / Theses on the topic 'Biosensors devices'

My research broadly covers various important aspects of microfluidic devices and biosensors. Specifically, this dissertation reports: (1) a new and effective room temperature method of bonding polydimethylsiloxane (PDMS) microfluidics to substrates such as silicon and glass, (2) a new microfluidic pump concept and implementation specifically designed to repeatedly drive a small sample volume (<1 µL) very rapidly (~500 µL/min) through a sensor-containing flow channel to significantly decrease sensor response time through advection-driven rather than diffusion-driven mass transport, (3) use of a new microfluidic material based on polyethylene glycol diacrylate (PEGDA) to implement impedance-based dynamic nanochannel sensors for protein sensing, and (4) an investigation of galvanoluminescence and how to avoid it for conditions important to fluorescence-based dielectrophoresis (DEP) microfluidic biosensors. Over the last decade, the Nordin research group has developed a lab-on-a-chip (LOC) biosensor based on silicon photonic microcantilever arrays integrated with polydimethylsiloxane (PDMS) microfluidics for protein biomarker detection. Integration requires reliable bonding at room temperature with adequate bond strength between the PDMS element and microcantilever sensor substrate. The requirement for a room temperature process is particularly critical because microcantilevers must be individually functionalized with antibody-based receptor molecules prior to bonding and cannot withstand significant heating after functionalization. I developed a new room temperature bonding method using PDMS curing agent as an intermediate adhesive layer. Two curing agents (Sylgard 184 and 182) were compared, as well as an alternate UV curable adhesive (NOA 75). The bond strength of Sylgard 184 was found to be stronger than Sylgard 182 under the same curing conditions. Overnight room temperature curing with Sylgard 184 yields an average burst pressure of 433 kPa, which is more than adequate for many PDMS sensor devices. In contrast, UV curable epoxy required a 12 hour bake at 50 °C to achieve maximum bond strength, which resulted in a burst pressure of only 124 kPa. In many biosensing scenarios it is desirable to use a small sample volume (<1 µL) to detect small analyte concentrations in as short a time as possible. I report a new microfluidic pump to address this need, which we call a reflow pump. It is designed to rapidly pump a small sample volume back and forth in a flow channel. Ultimately, the flow channel would contain functionalized sensor surfaces. The rapid flow permits use of advection-driven mass transport to the sensor surfaces to dramatically reduce sensor response times compared to diffusion-based mass transport. Normally such rapid flow would have the effect of decreasing the fraction of analyte molecules in the volume that would see the sensor surfaces. By configuring the pump to reflow fluid back and forth in the flow channel, the analyte molecules in the small sample volume are used efficiently in that they have many opportunities to make it to the sensor surfaces. I describe a 3-layer PDMS reflow pump that pumps 300 nL of fluid at 500 µL/min for 15 psi actuation pressure, and demonstrate a new two-layer configuration that significantly simplifies pump fabrication. Impedance-based nanochannel sensors operate on the basis of capturing target molecules in nanochannels such that impedance through the nanochannels is increased. While simple in concept, the response time can be quite long (8~12 hours) because the achievable flow rate through a nanochannel is very limited. An approach to dramatically increase the flow rate is to form nanochannels only during impedance measurements, and otherwise have an array of nanotrenches on the surface of a conventional microfluidic flow channel where they are exposed to normal microfluidic flow rates. I have implemented such a dynamic nanochannel approach with a recently-developed microfluidic material based polyethylene glycol diacrylate (PEGDA). I present the design, fabrication, and testing of PEGDA dynamic nanochannel array sensors, and demonstrate an 11.2 % increase in nanochannel impedance when exposed to 7.2 µM bovine serum albumin (BSA) in phosphate buffered saline (PBS). Recently, LOC biosensors for cancer cell detection have been demonstrated based on a combination of dielectrophoresis (DEP) and fluorescence detection. For fluorescence detection it is critical to minimize other sources of light in the system. However, reported devices use a non-noble metal electrode, indium tin oxide (ITO), to take advantage of its optical transparency. Unfortunately, use of non-noble metal electrodes can result in galvanoluminescence (GL) in which the AC voltage applied to the electrodes to achieve DEP causes light emission, which can potentially confound the fluorescence measurement. I designed and fabricated two types of devices to examine and identify conditions that lead to GL. Based on my observations, I have developed a method to avoid GL that involves measuring the impedance spectrum of a DEP device and choosing an operating frequency in the resistive portion of the spectrum. I also measure the emission spectrum of twelve salt solutions, all of which exhibited broadband GL. Finally, I show that in addition to Au, Cr and Ni do not exhibit GL, are therefore potentially attractive as low cost DEP electrode materials.

In recent years, the LOC community has focused most of its research in the biomedical and biotechnology fields, due to the need of portable, low power consumption and low cost theranostics microdevices. Some developing countries do not have suitable medical diagnostics technologies and the supply and storage of the reagents is in many cases limited as well as the access to energy. Furthermore, developed countries are experimenting population aging needing novel low cost efficient disease-screening technologies. The introduction of LOC and microfluidics allow the integration of complex functions that could lead to the developing of more accurate, cheap and reliable theranostic tools. Current focus of application is focused mostly in drug delivery 1, cellular analysis 2, and disease diagnosis 3. Microfluidics is improving the developing of novel point-of-care devices, but there are some challenges that are slowing down the massive production of these LOC. These areas include new methods for sample collection, world-to-chip interfaces, sample pre-treatment, improvement of long-term stability of reagents, working with complex sample specimens, multiple detection of biomarkers and simplify the read-out 4. The main aim of this thesis work was to create novel, cheap and with a high degree of automatization miniaturized biosensing devices with the objective to facilitate Point-of-Care diagnostics in the near future. Our efforts have been focused into developing a LOC system with electrochemical sensing capabilities adjustable to any biomarker, depending only on sample volumes and required analysis times. The devices integrate low-cost label-free biosensors exploiting microfluidics-based self-functionalization, or specialization. The biosensor functionalization takes place in situ and selectively, just before the sensing, and their area keeps dry and inactive until the test starts. The reagents and the sensing parts are kept separated and brought into contact just before the test, avoiding the need of complex fabrication and storage methods to guarantee functionalization integrity. The novel design reduces the cost of the final instrumentation, by simplifying the measurements, while keeping sensitivities and LODs relevant for the application. Furthermore, since the interaction of antibody and protein is time and concentration dependent, our device has the capability to adjust its sensitivity. We have tuned and characterized our system sensitivity using different biomarkers. The development of our novel devices was possible by exploiting synergies in disciplines previously studied in our group. Particularly, in fields such as microfluidics 5-8, surface functionalization 9-14 and electrochemical biosensors 15-19. Summarizing, we are proposing novel microfluidic devices with integrated biosensors. The systems are based on the principle of laminar co-flow in order to perform an on-chip selective surface bio-functionalization of LOC integrated biosensors. This method has the advantage of performing the surface modification protocols “in situ” before the detection. The system can be easily scaled to incorporate several sensors with different biosensing targets in a single chip. We are proposing a novel voltage and impedance differential measurements; that allow us to simplify the read-out. As biomedical application we focus our attention on the detection of prostate cancer biomarkers. Bibliography 1. I. U. Khan, C. A. Serra, N. Anton and T. Vandamme, Journal of Controlled Release, 2013, 172, 1065-1074. 2. H. Andersson and A. Van den Berg, Sensors and Actuators B: Chemical, 2003, 92, 315-325. 3. M. J. Cima, Annual Review of Chemical and Biomolecular Engineering, 2011, 2, 355-378. 4. C. D. Chin, V. Linder and S. K. Sia, Lab on a Chip, 2012, 12, 2118-2134. 5. R. Rodriguez-Trujillo, C. A. Mills, J. Samitier and G. Gomila, Microfluidics and Nanofluidics, 2007, 3, 171-176. 6. R. Rodriguez-Trujillo, O. Castillo-Fernandez, M. Garrido, M. Arundell, A. Valencia and G. Gomila, Biosensors and Bioelectronics, 2008, 24, 290-296. 7. O. Castillo-Fernandez, R. Rodriguez-Trujillo, G. Gomila and J. Samitier, Microfluidics and Nanofluidics, 2014, 16, 91-99. 8. J. Comelles, V. Hortigüela, J. Samitier and E. Martínez, Langmuir, 2012, 28, 13688-13697. 9. E. Prats-Alfonso, F. García-Martín, N. Bayo, L. J. Cruz, M. Pla-Roca, J. Samitier, A. Errachid and F. Albericio, Tetrahedron, 2006, 62, 6876-6881. 10. J. Vidic, M. Pla-Roca, J. Grosclaude, M.-A. Persuy, R. Monnerie, D. Caballero, A. Errachid, Y. Hou, N. Jaffrezic-Renault, R. Salesse, E. Pajot-Augy and J. Samitier, Analytical Chemistry, 2007, 79, 3280-3290. 11. Y. Hou, S. Helali, A. Zhang, N. Jaffrezic-Renault, C. Martelet, J. Minic, T. Gorojankina, M.-A. Persuy, E. Pajot-Augy, R. Salesse, F. Bessueille, J. Samitier, A. Errachid, V. Akimov, L. Reggiani, C. Pennetta and E. Alfinito, Biosensors and Bioelectronics, 2006, 21, 1393-1402. 12. S. Rodríguez Seguí, M. Pla, J. Minic, E. Pajot‐Augy, R. Salesse, Y. Hou, N. Jaffrezic‐Renault, C. A. Mills, J. Samitier and A. Errachid, Analytical Letters, 2006, 39, 1735-1745. 13. A. Lagunas, J. Comelles, E. Martínez and J. Samitier, Langmuir, 2010, 26, 14154-14161. 14. A. Lagunas, J. Comelles, S. Oberhansl, V. Hortigüela, E. Martínez and J. Samitier, Nanomedicine: Nanotechnology, Biology and Medicine, 2013, 9, 694-701. 15. M. Castellarnau, N. Zine, J. Bausells, C. Madrid, A. Juárez, J. Samitier and A. Errachid, Materials Science and Engineering: C, 2008, 28, 680-685. 16. M. Castellarnau, N. Zine, J. Bausells, C. Madrid, A. Juárez, J. Samitier and A. Errachid, Sensors and Actuators B: Chemical, 2007, 120, 615-620. 17. M. Kuphal, C. A. Mills, H. Korri-Youssoufi and J. Samitier, Sensors and Actuators B: Chemical, 2012, 161, 279-284. 18. D. Caballero, E. Martinez, J. Bausells, A. Errachid and J. Samitier, Analytica Chimica Acta, 2012, 720, 43-48. 19. M. Barreiros dos Santos, J. P. Agusil, B. Prieto-Simón, C. Sporer, V. Teixeira and J. Samitier, Biosensors and Bioelectronics, 2013, 45, 174-180.
En años recientes, la comunidad de LOC ha enfocado todos sus esfuerzos en la investigación de nuevas aplicaciones para la biomedicina y biotecnología. Algunos países en vías de desarrollados no tienen tecnologías de diagnóstico adecuadas, además el suministro y almacenamiento de los reactivos es en muchos casos limitado, y en ocasiones cuentan con un acceso limitado al consumo de energía. Por otra parte, los países desarrollados se han encontrado con una población envejecida, y por lo tanto se ha generado la necesidad de contar con nuevas tecnologías para el diagnóstico de enfermedades las cuales sean accesibles y orientadas a una terapia más personalizada. Tanto la microfluídica como los LOC han permitido la integración de funciones de análisis complejas capaces de desarrollar herramientas de diagnostico más precisas, de bajo coste y confiables. Actualmente toda la atención se ha centrado en el diseño de aplicaciones para administración de fármacos 1, análisis celular 2 y diagnostico de enfermedades 3. La introducción de la microfluídica ha servido para mejorar el desarrollo de nuevos dispositivos point-of-care, pero todavía existen algunos problemas que han evitado la producción masiva de estos LOC. Las áreas en las que se pretende conseguir una mejora son la recolección de la muestra, mejora de la interfaz entre el chip y el usuario, tratamiento previo de la muestra, mejorar la estabilidad de los reactivos, trabajo con muestras complejas, detección múltiple de biomarcadores y simplificación del sistema de medida 4. Nuestros esfuerzos se han dedicado en desarrollar un sistema LOC con capacidad de detección electroquímica ajustable a cualquier biomarcador, dependiendo únicamente en la cantidad de muestra y los tiempos de análisis. Nuestros dispositivos microfluídicos cuentan con biosensores integrados de bajo coste con capacidad de auto-funcionalización. La funcionalización de los biosensores se realiza in-situ y selectivamente, antes de la detección, manteniendo el área de detección inerte hasta el inicio de la prueba. Los reactivos y el área de detección se almacenan por separado y entran en contacto hasta el inicio del experimento, lo cual facilita el método de fabricación. Se ha podido desarrollar este trabajo gracias a los estudios previos realizados en nuestro grupo en distintas disciplinas, tales como: microfluídica 5-8, funcionalización de superficies 9-14 y biosensores electroquímicos 15-19. Bibliografía 1. I. U. Khan, C. A. Serra, N. Anton and T. Vandamme, Journal of Controlled Release, 2013, 172, 1065-1074. 2. H. Andersson and A. Van den Berg, Sensors and Actuators B: Chemical, 2003, 92, 315-325. 3. M. J. Cima, Annual Review of Chemical and Biomolecular Engineering, 2011, 2, 355-378. 4. C. D. Chin, V. Linder and S. K. Sia, Lab on a Chip, 2012, 12, 2118-2134. 5. R. Rodriguez-Trujillo, C. A. Mills, J. Samitier and G. Gomila, Microfluidics and Nanofluidics, 2007, 3, 171-176. 6. R. Rodriguez-Trujillo, O. Castillo-Fernandez, M. Garrido, M. Arundell, A. Valencia and G. Gomila, Biosensors and Bioelectronics, 2008, 24, 290-296. 7. O. Castillo-Fernandez, R. Rodriguez-Trujillo, G. Gomila and J. Samitier, Microfluidics and Nanofluidics, 2014, 16, 91-99. 8. J. Comelles, V. Hortigüela, J. Samitier and E. Martínez, Langmuir, 2012, 28, 13688-13697. 9. E. Prats-Alfonso, F. García-Martín, N. Bayo, L. J. Cruz, M. Pla-Roca, J. Samitier, A. Errachid and F. Albericio, Tetrahedron, 2006, 62, 6876-6881. 10. J. Vidic, M. Pla-Roca, J. Grosclaude, M.-A. Persuy, R. Monnerie, D. Caballero, A. Errachid, Y. Hou, N. Jaffrezic-Renault, R. Salesse, E. Pajot-Augy and J. Samitier, Analytical Chemistry, 2007, 79, 3280-3290. 11. Y. Hou, S. Helali, A. Zhang, N. Jaffrezic-Renault, C. Martelet, J. Minic, T. Gorojankina, M.-A. Persuy, E. Pajot-Augy, R. Salesse, F. Bessueille, J. Samitier, A. Errachid, V. Akimov, L. Reggiani, C. Pennetta and E. Alfinito, Biosensors and Bioelectronics, 2006, 21, 1393-1402. 12. S. Rodríguez Seguí, M. Pla, J. Minic, E. Pajot‐Augy, R. Salesse, Y. Hou, N. Jaffrezic‐Renault, C. A. Mills, J. Samitier and A. Errachid, Analytical Letters, 2006, 39, 1735-1745. 13. A. Lagunas, J. Comelles, E. Martínez and J. Samitier, Langmuir, 2010, 26, 14154-14161. 14. A. Lagunas, J. Comelles, S. Oberhansl, V. Hortigüela, E. Martínez and J. Samitier, Nanomedicine: Nanotechnology, Biology and Medicine, 2013, 9, 694-701. 15. M. Castellarnau, N. Zine, J. Bausells, C. Madrid, A. Juárez, J. Samitier and A. Errachid, Materials Science and Engineering: C, 2008, 28, 680-685. 16. M. Castellarnau, N. Zine, J. Bausells, C. Madrid, A. Juárez, J. Samitier and A. Errachid, Sensors and Actuators B: Chemical, 2007, 120, 615-620. 17. M. Kuphal, C. A. Mills, H. Korri-Youssoufi and J. Samitier, Sensors and Actuators B: Chemical, 2012, 161, 279-284. 18. D. Caballero, E. Martinez, J. Bausells, A. Errachid and J. Samitier, Analytica Chimica Acta, 2012, 720, 43-48. 19. M. Barreiros dos Santos, J. P. Agusil, B. Prieto-Simón, C. Sporer, V. Teixeira and J. Samitier, Biosensors and Bioelectronics, 2013, 45, 174-180.

Conjugated polymers have brought about a revolution in the world of polymers and hence, opened up new possibilities in the utilization of polymers in ways hitherto unknown. As a result of the conjugated bonds present, they are able to carry electrons and therefore mimic metals. One of the objectives of this work is the syntheses of processable conductive polymers in a cost effective manner that would still have desired physical and chemical properties. A series of electroative polymers have been prepared and most of these are intrinsically conductive. A semiconducting filler, single-walled carbon nanotubes, was added to impart conductivity to the functional polymer, α,ω-bi[2,4-dinitrophenyl caproic] [poly(ethyleneoxide)-b-poly(2-methoxystyrene)-b-poly(ethylene oxide)] which is non-conducting. Composites of this polymer with polystyrene and SWCNTs were electrospun to form nanofiber mats which had mixed morphologies but predominantly beaded. The nanofibers ranged in diameter form ~ 65 to ~ 500 nm. These functional nanofibers were incubated in fluorescently (FITC) tagged Immunoglobulin E, IgE and they showed biospecificity towards IgE. The current-voltage characteristics indicated a change in behavior when bound to IgE and otherwise. The intrinsically conductive polymers of 3-alkylthiophenes were prepared using the Grignard metathesis reaction, oxidative coupling with ferric chloride as well as copolymerization via ATRP with conductive P3DT as the macroinitiator. These environmentally stable polymers show a glass transition mostly between 48 to 50 °C and the π to π* transition of the conjugated polymers is evidenced in wavelength of their absorption in the UV/Vis/NIR as the spectra indicated. The particle sizes obtained by light scattering showed average diameter between 28 to 40 nm for the different polymers. Electrochemical studies on the block copolymer and random polymer series by cyclic voltammetry show the species are redox active in solution. Conductivity of multiwall nanotubes/ P3MT composite series showed conductivity values between 1.3 x 10-7 to 2.5 x 10-4 S/cm as determined from the bulk resistance measurements of pressed pellets of the composites. The biofunctional polymers investigated are highly promising in the biotechnology/biomedical industry as potential biosensors. The non-biofunctional polymers too are applicable in photovoltaics, optoelectronics, energy storage, solar cells, the semiconductor industry and many more.

Aquesta tesi doctoral té com a objectiu el desenvolupament de diversos biosensors que operen sense necessitat de marcatge addicional basats en dispositius plasmònics òptics per a la detecció directa de medicaments o biomarcadors relacionats amb diferents malalties i que són analitzats directament en mostres humanes com plasma, sèrum, orina o esput. Aquests dispositius biosensors ofereixen un sens fi de beneficis com és la seva alta sensibilitat, facilitat d’operació, l’obtenció de dades quantitatives, detecció sense marcatge en temps real, i comunament només necessiten d’un petit volum de mostra. Tot això converteix els biosensors plasmònics en eines analítiques molt adequades per al diagnòstic de malalties, el control de la medicació o el seguiment de teràpies personalitzades. El nostre grup d’investigació ha demostrat amb èxit la implementació de biosensors òptics basats en plasmònica i en fotònica de silici, inclòs el desenvolupament complet de bioaplicaciones, el que ha aplanat el camí de la seva futura transferència tecnològica per a la seva implementació com a dispositius Point-of-Care ( POC). Els biosensors desenvolupats en aquesta Tesi inclouen la seva optimització i validació completa amb mostres reals, exemplificant alguns desafiaments clínics en els quals aquests biosensors plasmònics poden superar importants limitacions de les tècniques d’anàlisi convencionals actuals, mostrant el seu potencial i versatilitat com a futurs dispositius POC per ser usats en les unitats d’atenció primària en salut o fins i tot en l’entorn domèstic per al propi autocontrol per part dels pacients. La tesi està organitzada en sis capítols. El capítol 1 conté la introducció dels conceptes bàsics i l’estat de l’art sobre els avenços actuals en les tècniques de diagnòstic i control de malalties i / o teràpies i el paper que exerceixen els biosensors per millorar-los. El capítol 2 inclou una descripció detallada de les plataformes biosensoras emprades i una descripció general dels processos metodològics. El Capítol 3 descriu el desenvolupament d’un dispositiu nanoplasmónico per al control terapèutic de l’medicament acenocumarol, un anticoagulant comunament administrat directament en plasma humà. El Capítol 4 es centra en el desenvolupament d’un biosensor plasmónico que serveixi com a control de la dieta lliure de gluten que han de portar els pacients celíacs. El Capítol 5 descriu les estratègies desenvolupades per a la detecció de dos biomarcadors per al diagnòstic primerenc de tuberculosi en mostres d’esput. Finalment, el Capítol 6 explora la detecció de quatre autoanticossos específics associats amb l’aparició de l’tumor directament en el sèrum humà com biomarcadors potencials per al diagnòstic primerenc de el càncer colorectal.
Esta Tesis Doctoral tiene como objetivo el desarrollo de diversos biosensores que operan sin necesidad de marcaje adicional basados en dispositivos plasmónicos ópticos para la detección directa de medicamentos o biomarcadores relacionados con diferentes enfermedades y que son analizados directamente en muestras humanas como plasma, suero, orina o esputo. Estos dispositivos biosensores ofrecen un sinnúmero de beneficios como es su alta sensibilidad, facilidad de operación, la obtención de datos cuantitativos, detección sin marcaje en tiempo real, y comúnmente sólo necesitan de un pequeño volumen de muestra. Todo esto convierte a los biosensores plasmónicos en herramientas analíticas muy adecuadas para el diagnóstico de enfermedades, el control de la medicación o el seguimiento de terapias personalizadas. Nuestro grupo de investigación ha demostrado exitosamente la implementación de biosensores ópticos basados en plasmónica y en fotónica de silicio, incluido el desarrollo completo de bioaplicaciones, lo que ha allanado el camino de su futura transferencia tecnológica para su implementación como dispositivos Point-of-Care (POC). Los biosensores desarrollados en esta Tesis incluyen su optimización y validación completa con muestras reales, ejemplificando algunos desafíos clínicos en los que dichos biosensores plasmónicos pueden superar importantes limitaciones de las técnicas de análisis convencionales actuales, mostrando su potencial y versatilidad como futuros dispositivos POC para ser usados en las unidades de atención primaria en salud o incluso en el entorno doméstico para el propio autocontrol por parte de los pacientes. La tesis está organizada en seis capítulos. El Capítulo 1 contiene la introducción de los conceptos básicos y el estado del arte sobre los avances actuales en las técnicas de diagnóstico y control de enfermedades y/o terapias y el papel que desempeñan los biosensores para mejorarlos. El Capítulo 2 incluye una descripción detallada de las plataformas biosensoras empleadas y una descripción general de los procesos metodológicos. El Capítulo 3 describe el desarrollo de un dispositivo nanoplasmónico para el control terapéutico del medicamento acenocumarol, un anticoagulante comúnmente administrado directamente en plasma humano. El Capítulo 4 se centra en el desarrollo de un biosensor plasmónico que sirva como control de la dieta libre de gluten que deben llevar los pacientes celíacos. El Capítulo 5 describe las estrategias desarrolladas para la detección de dos biomarcadores para el diagnóstico temprano de tuberculosis en muestras de esputo. Finalmente, el Capítulo 6 explora la detección de cuatro autoanticuerpos específicos asociados con la aparición del tumor directamente en el suero humano como biomarcadores potenciales para el diagnóstico temprano del cáncer colorrectal.
This Doctoral Thesis aims to the development of several label-free biosensing analytical strategies integrated within optical plasmonic devices for the direct detection of drugs or biomarkers related to different diseases in biological samples such as plasma, serum, urine, and sputum. These biosensor devices offer several benefits like their high sensitivity, ease of operation, quantitative data, label-free operation, and real-time detection, and commonly require a small sample volume. All this turn plasmonic biosensors into well-suited analytical tools for diagnosing diseases, monitoring medication, or for personalized therapies follow-up. Our research group has extensively demonstrated the successful conjunction of novel in-house optical biosensor configurations (like plasmonic and photonic-based designs) with the full demonstrations of bioapplications, which has paved the way for their potential technological transfer as Point-of-Care devices (POC) for clinical diagnostics. The biosensor assays here implemented, which include their full optimization and validation with real samples, exemplify clinical challenges where such biosensors can overcome limitations of current conventional analytical techniques. The results show the potential and versatility that plasmonic biosensors can offer as future POC devices placed in primary healthcare units or even in the household environment for patients’ self-monitoring. This thesis is organized into six chapters. Chapter 1 is the introductory one, which explains the basic concepts and the state of the art of the current advances in diagnosis and monitoring techniques of diseases and/or therapies and the role of biosensors to improve them. Chapter 2 includes a detailed description of the biosensor platforms employed and a general description of the methodological processes. Chapter 3 is related to the development of a nanoplasmonic device for the therapeutic monitoring of the drug acenocoumarol, a commonly administered anticoagulant, directly in human plasma. Chapter 4 focuses on the implementation of a plasmonic biosensor that monitors the gluten-free diet in urine in celiac patients. Chapter 5 describes the biosensing strategies developed for the detection of two biomarkers for the early diagnosis of tuberculosis in sputum samples. Finally, Chapter 6 explores the detection of four specific autoantibodies associated with the tumor onset directly in human serum as potential biomarkers for the early detection of colorectal cancer.
Universitat Autònoma de Barcelona. Programa de Doctorat en Química

Along with an increasing understanding of the harmful effects on the environment of a wide range of pollutants has come the need for more sensitive, faster and less expensive detection methods of identification and quantitation. Many environmental pollutants occur in low levels and often in complex matrices thus analysis can be difficult, time consuming and costly. Because of the availability and easy cultivation of the microorganisms with potentially high specificity, there is considerable interest in the use of living microorganisms as the analytical component (the biocomponent) of sensors for pollutants. While a number of biosensors using bacteria have been developed, yeast has been comparatively rarely used as the biocomponent. Yeast are attractive because they are easy to culture and they are eukaryotes which means their biochemistry is in many respects closer to that of higher organisms. This thesis describes the development of whole cell bioassays that use yeast cells as a sensing element and redox mediators to probe the intracellular redox reactions to monitor the catabolic activity of the yeast resulting from the external substrate, steady-state voltammetry is utilised as the electrochemical detection technique. The isogenic differential enzyme analysis (IDEA) concept of Lincoln Ventures Limited, lead NERF funded research consortium uses bacteria that have been cultured using specific organic pollutants as the carbon source which are the biocomponent in sensors. The use of wild type yeast Arxula adeninivorans that has the ability to use a very wide variety of substrates as sources of carbon and nitrogen was used as an alternative to bacteria to validate the “IDEA” concept. Naphthalene and di-butyl phthalate were chosen as model target contaminant molecules. The performance, detection limits and the usefulness of yeast based biosensor applications for environmental analysis are discussed. This thesis also describes the development and optimisation of a simple, cost effective in vivo estrogens bioassay for the detection of estrogens using either genetically modified or a wild type yeast Saccharomyces cerevisiae. In this study, catabolic repression by glucose was exploited to achieve specificity to estrogens in complex environmental samples that eliminates the requirement for conventional sample preparation. This is the first time that the use of wild type yeast to quantify estrogens has been reported. The attractive features of the bioassay are its use of a non-GMO organism, its speed, its high specificity and sensitivity with a detection limit of 10-15 M. The similarity of binding affinities for major estrogens to those of human estrogens receptors makes this in vivo estrogen bioassay very useful for analytical/screening procedures. The electrochemical detection method also makes it easy to interface with a variety of electronic devices.

In dieser Arbeit wurden mit Hilfe einer Kombination aus „metal assisted chemical etching“ (MACE) und Polystyrol-Nanopartikel-Lithographie, Säulen-strukturierte Siliziumoberflächen mit verschiedenen Säulendurchmessern und –längen, wie auch unterschiedlichen Säulenabständen, synthetisiert. Das im Anschluss durchgeführte Elektropolier-Verfahren verhalf dabei, die durch den MACE-Prozess erhöhte Oberflächendefektdichte (DSS) zu reduzieren. Dieses Verfahren wurde von in situ Photolumineszenzmessungen unterstützt. Eine im Anschluss an das Elektropolierverfahren durchgeführte Methylpassivierung erwies sich als notwendig, um den Zustand der reduzierten DSS für einen längeren Zeitraum an Luft stabil zu halten. Die elektropolierten und methylpassivierten Oberflächen wurden als Substrate in Kombination mit dem leitfähigen Polymer PEDOT:PSS für die Herstellung von Hybridsolarzellen verwendet. Im Vergleich zu Zellen deren strukturierte Oberfläche nicht zuvor elektropoliert worden ist, kam es bei den zusätzlich elektropolierten Zellen zu einer Effizienzverbesserung und einer Erhöhung des Kurzschlussstroms (JSC). Elektrochemische Verfahren zur Veränderung der Säulen-Morphologie sind in dieser Arbeit ebenfalls untersucht worden. Um eine strukturierte Oberfläche auch in anderen Bereichen, wie etwa der Biosensorik, verwenden zu können, bedarf es neben der Methylpassivierung weiterer Formen der Funktionalisierung. Im Rahmen dieser Arbeit wurde ein Syntheseweg entwickelt, der es ermöglicht direkt an das Siliziumsubstrat gebundene Hydroxylgruppen zu erhalten, ohne dass es zu einer Bildung von intermediären Oxidschichten zwischen Substrat und den Hydroxylgruppen kommt. Diese wurden anschließend mit verschiedenen Silanen umgesetzt, um organische Gruppen an die Oberfläche zu binden. Die gebundenen Silanderivate können im Folgenden weiter modifiziert werden, um die selektive Anbindung von Biomolekülen zu ermöglichen.
Within this work, the “metal assisted chemical etching” (MACE) technique was combined with shadow nanosphere lithography to fabricate nanowire structured Si surfaces with different wire lengths and diameters. Electropolishing procedures subsequent to the wire growth resulted in a reduction of the surface defect density (DSS). The electropolishing procedure was directly monitored with the help of in situ photoluminescence spectroscopy. Previous works already observed a full and air stable surface passivation of flat Si surfaces by methylation. Also in the present work, the nanowire surfaces were methylated after the electropolishing procedure to preserve the reduced DSS. To determine the impact of this method on the solar cell performance, the electropolished and methylated surfaces were combined with the conductive polymer PEDOT:PSS. It revealed that the cells with the electropolished substrates exhibit a higher efficiency and an increased short circuit current (JSC). Different electrochemical procedures to change the wire morphology after the structuring have been investigated as well. To use the Si substrates for applications such as biosensing, different passivation/functionalization techniques besides the methylation are required. In this thesis, a new functionalization procedure was developed to obtain air stable hydroxyl groups that are directly bound to the Si substrate without an intervening oxide layer. To demonstrate the possibility to use these hydroxyl groups in the same way as the hydroxyl groups present on a Si oxide layer, further modifications with different silane species, such as APTES and AMMS, were conducted. In order to generate a more selective anchor group, the bound APTES molecules were further modified by a maleimide derivative, which allow for the selective binding of thiol-containing molecules.

Developing non-invasive and accurate diagnostics that are easily manufactured, robust and reusable will provide monitoring of high-risk individuals in any clinical or point-of-care environment, particularly in the developing world. There is currently no rapid, low-cost and generic sensor fabrication technique capable of producing narrow-band, uniform, reversible colorimetric readouts with a high-tuneability range. This thesis aims to present a theoretical and experimental basis for the rapid fabrication, optimisation and testing of holographic sensors for the quantification of pH, organic solvents, metal cations, and glucose in solutions. The sensing mechanism was computationally modelled to optimise its optical characteristics and predict the readouts. A single pulse of a laser (6 ns, 532 nm, 350 mJ) in holographic “Denisyuk” reflection mode allowed rapid production of sensors through silver-halide chemistry, in situ particle size reduction and photopolymerisation. The fabricated sensors consisted of off-axis Bragg diffraction gratings of ordered silver nanoparticles and localised refractive index changes in poly(2-hydroxyethyl methacrylate) and polyacrylamide films. The sensors exhibited reversible Bragg peak shifts, and diffracted the spectrum of narrow-band light over the wavelength range λpeak ≈ 500-1100 nm. The application of the holographic sensors was demonstrated by sensing pH in artificial urine over the physiological range (4.5-9.0), with a sensitivity of 48 nm/pH unit between pH 5.0 and 6.0. For sensing metal cations, a porphyrin derivative was synthesised to act as the crosslinker, the light absorbing material, the component of a diffraction grating, as well as the cation chelating agent. The sensor allowed reversible quantification of Cu2+ and Fe2+ ions (50 mM - 1 M) with a response time within 50 s. Clinical trials of a glucose sensor in the urine samples of diabetic patients demonstrated that the glucose sensor has an improved performance compared to a commercial high-throughput urinalysis device. The experimental sensitivity of the glucose sensor exhibited a limit of detection of 90 µM, and permitted diagnosis of glucosuria up to 350 mM. The sensor response was achieved within 5 min and the sensor could be reused about 400 times without compromising its accuracy. Holographic sensors were also tested in flake form, and integrated with paper-iron oxide composites, dyed filter and chromatography papers, and nitrocellulose-based test strips. Finally, a generic smartphone application was developed and tested to quantify colorimetric tests for both Android and iOS operating systems. The developed sensing platform and the smartphone application have implications for the development of low-cost, reusable and equipment-free point-of-care diagnostic devices.

Thesis (M.S.)--West Virginia University, 1999.
Title from document title page. Document formatted into pages; contains x, 126 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. [72]-75).

Suspended lipid bilayers, or black lipid membranes (BLMs), have been used to study the electrophysiological properties of ion channels (ICs); however, BLMs assembled from natural, non-polymerizable lipids are inherently unstable due to the non-covalent associations on which they are based. Lifetimes of several hours are commonly observed in BLMs until rupture due to mechanical, thermal, or chemical insults. One potential improvement is the use of polymerizable phospholipids (poly(lipids)). BLMs prepared using dienoyl functionalized poly(lipids) and binary mixtures of fluid, non-polymerizable lipids with poly(lipids) were investigated for IC recordings.poly(BLMs) exhibited enhanced lifetimes from several hours to upwards of 4 weeks while maintaining IC functionality for one week. Activity of ICs that require membrane fluidity was retained using binary phospholipid mixtures of fluid and polymeric phospholipids. IC activity was retained by inducing domain formation, wherein ICs incorporated into the fluid domains. The binary membranes exhibited marked enhancement in stability resulting from fractional poly(lipids) polymerization. Additionally, ICs can be reconstituted into the fluid domains following photopolymerization and subsequent domain formation, a key requirement when UV-sensitive ICs are utilized. Here, the electrical properties, stability, and incorporation of pore-forming ICs, including hemolysin, alamethicin, and gramicidin, into poly(lipid) membranes are reported. Potential applications developing ligand-gated IC based sensors for high throughput screening are being investigated.In parallel to the characterization of poly(lipids) for potential long-term IC membranes, a model ligand-gated IC was expressed, characterized, and reconstituted into non-polymerizable lipids. Mutant K_ATP channels were expressed in mammalian and yeast systems. The orientations of mutant K_ATP channels were studied using electrophysiological and immunohistochemical techniques. Large quantities were expressed and purified from Pichia pastoris and functionally reconstituted into BLMs. ATP and long-chaing coenzyme A ester sensitivity was maintained in reconstituted in BLMs. K_ATP channels will serve as a model system for testing the effect of poly(lipid) BLMs on IC function. Future utilization of poly(lipid) BLMs in combination with ligand-gated ICs offer major advancements to potential increased throughput for IC screening.

The engineering of biology strives on the creation of biological devices concerning society-impact applications. In this PhD thesis, we developed mathematical and experimental tools for the standard and rational design of living devices for biomedical purposes, offering robust and reliable responses. By breaking-up cellular device complexity into functional modules, we have analysed how extracellular information is detected, processed and transformed thanks to re-engineering intrinsic cellular components. We show how the desired range of action of a biosensor could be tuned by modifying the relative levels from two-component receptors’ biosensors. Regarding information processing, combining multicellularity and space permits to develop a 2D multi-branch approach inspired from printed electronics, allowing to perform logic computation by transferring device complexity into the geometrical arrangement. Sensing and processing capabilities have been applied as a proof-of-concept for the design of cellular devices for Diabetes Mellitus. Treating the cellular device closed-loop response as the fourth-functional module allowed to in silico decipher device characteristics on glycaemia regulation and design novel strategies based on dietary modulation, putting the manifest the need to combine both experimental and computational tools for living device application-based designs.
L’aplicació de principis d’enginyeria en biologia permet somniar en l’ús de dispositius biològics per abordar problemes de la societat. Concretament, en aquesta tesi doctoral, s’ha abordat el disseny de dispositius biològics per aplicacions biomèdiques mitjançant la combinació d’eines experimentals i computacionals. La creació d’aquests dispositius demana d’un disseny racional que ofereixi respostes robustes i fiables. L’estudi de la creació de dispositius biològics s’ha fet seguint una aproximació modular, on s’ha analitzat com es poden re-enginyeritzar components cel·lulars per obtenir una resposta que s’adeqüi a l’aplicació requerida. Hem demostrat com podem modular el rang de detecció de la capa sensora a través de la modulació de l’element receptor de sensors bastats en dos components. Hem analitzat com integrar informació de diferents fonts de manera sistemàtica i robusta introduint com a nou element de computació l’espai i la divisió de tasques; tot desenvolupant un marc teòric i validant experimentalment per un seguit de funcions lògiques. Finalment, hem desenvolupat dispositius biològics que responen a molècules fisiològiques. Concretament, hem abordat el disseny de dispositius biològics pel tractament de la Diabetes Mellitus. Una primera validació experimental ens ha permès establir l’ús d’aquests dispositius in vitro. Seguidament, hem aprofundit en l’estudi de la seva aplicació mitjançant l’ús d’un simulador de pacient diabètic que ens ha permès el seu tractament virtual i l’anàlisi de les característiques del dispositiu per la regulació de la glicèmia. Finalment, hem explorat com la combinació dels dispositius cel·lulars amb la regulació del patró d’ingestes introdueix millores en els nivells de glucosa en sang. Posant de manifest el potencial que ofereix la creació d’una plataforma hibrida pel disseny de dispositius cel·lulars per una determinada aplicació.

De nos jours, efficacité et précision des diagnostics médicaux sont des éléments essentiels pour la prévention en termes de santé et permettre une prise en charge rapide des maladies des patients. Les récentes innovations technologiques, particulièrement dans les domaines de la microélectronique et des sciences des matériaux ont permis le développement de nouvelles plateformes personnalisées de diagnostics portatifs. Les matériaux électroniques organiques qui ont déjà par le passé démontré leur potentiel en étant intégrés dans des produits de grande consommation tels que les écrans de smartphones ou encore les cellules solaires montrent un fort potentiel pour une intégration dans des dispositifs biomédicaux. En effet, de par leurs natures et leurs propriétés physiques et chimiques, ils peuvent être à la fois en contact avec les milieux biologiques et constituer l’interface entre les éléments biologiques à l’étude, et les dispositifs électroniques. L’objectif de mes travaux de thèse et d’étudier et évaluer les performances des matériaux organiques électroniques intégrés dans des dispositifs biomédicaux en étudiant leurs interactions avec des milieux biologiques et par l’utilisation et l’optimisation de ces dispositifs permettre la détection de métabolites tel que le glucose ou lactate par exemple. Pendant ma thèse, j’ai notamment créé une plateforme de diagnostics combinant à la fois microfluidique et électronique organique permettant la multi détection de métabolites présents dans des fluides corporels humains, j’ai également conçu des capteurs intégrant des transistors organiques au sein des circuits électroniques classiques afin de détecter la présence des cellules tumorales. D’autres applications biologiques ont également été envisagées telles que la détection d’acides nucléiques par l’utilisation d’une approche simple de biofonctionnalisation. Bien que l’objectif ma thèse était de de créer des capteurs biomédicaux en utilisant une approche in vitro, il pourrait être également possible d’intégrer ces dispositifs « in vivo » ou encore dans des e-textiles
Rapid and early diagnosis of disease plays a major role in preventative healthcare. Undoubtedly, technological evolutions, particularly in microelectronics and materials science, have made the hitherto utopian scenario of portable, point-of-care personalized diagnostics a reality. Organic electronic materials, having already demonstrated a significant technological maturity with the development of high tech products such as displays for smartphones or portable solar cells, have emerged as especially promising candidates for biomedical applications. Their soft and fuzzy nature allows for an almost seamless interface with the biological milieu rendering these materials ideally capable of bridging the gap between electronics and biology. The aim of this thesis is to explore and validate the capabilities of organic electronic materials and devices in real-world biological sensing applications focusing on metabolite sensing, by combining both the right materials and device engineering. We show proof-of-concept studies including microfluidic integrated organic electronic platforms for multiple metabolite detection in bodily fluids, as well as more complex organic transistor circuits for detection in tumor cell cultures. We finally show the versatility of organic electronic materials and devices by demonstrating other sensing strategies such as nucleic acid detection using a simple biofunctionalization approach. Although the focus is on in vitro metabolite monitoring, the findings generated throughout this work can be extended to a variety of other sensing strategies as well as to applications including on body (wearable) or even in vivo sensing

The necessity of using extremely high sensitivity biosensors in certain research areas has remarkably increased during the last two decades. Optical structures, where light is used to transduce biochemical interactions into optical signals, are a very interesting approach for the development of this type of biosensors. Within optical sensors, photonic integrated architectures are probably the most promising platform to develop novel lab-on-a-chip devices. Such planar structures exhibit an extremely high sensitivity, a significantly reduced footprint and a high multiplexing potential for sensing applications. Furthermore, their compatibility with CMOS processes and materials, such as silicon, opens the route to mass production, thus reducing drastically the cost of the final devices. Optical sensors achieve their specificity and label-free operation by means of a proper chemical functionalization of their surfaces. The selective attachment of the receptors allows the detection of the target analytes within a complex matrix. This PhD Thesis is focused on the development of label-free photonic integrated sensors in which the detection is based on the interaction of the target analytes with the evanescent field that travels along the structures. Herein, we studied several photonic structures for sensing purposes, such as photonic crystals and ring resonators. Photonic crystals, where their periodicity provokes the appearance of multiple back and forth reflections, exhibits the so-called slow-light phenomenon that allows an increase of the interaction between the light and the target matter. On the other hand, the circulating nature of the resonant modes in a ring resonator offers a multiple interaction with the matter near the structure, providing a longer effective length. We have also proposed a novel approach for the interrogation of photonic bandgap sensing structures where simply the output power needs to measured, contrary to current approaches based on the spectral interrogation of the photonic structures. This novel technique consists on measuring the overlap between a broadband source and the band edge from a SOI-based corrugated waveguide, so that we can determine indirectly its spectral position in real-time. Since there is no need to employ tunable equipment, we obtain a lighter, simpler and a cost-effective platform, as well as a real-time observation of the molecular interactions. The experimental demonstration with antibody detection measurements has shown the potential of this technique for sensing purposes
García Castelló, J. (2014). A Novel Approach to Label-Free Biosensors Based on Photonic Bandgap Structures [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/35398
TESIS

Thesis (Ph.D.)--Biomedical Engineering, Georgia Institute of Technology, 2008.
Committee Chair: William D Hunt; Committee Member: Bruno Frazier; Committee Member: Dale Edmondson; Committee Member: Marie Csete; Committee Member: Peter Edmonson; Committee Member: Ruth O'Regan

Doctor of Philosophy
Department of Chemistry
Jun Li
Developing new and rapid methods for pathogen detection with enhanced sensitivity and temporal resolution is critical for protecting general public health and implementing the food and water safety standards. In this research vertically aligned carbon nanofiber nanoelectrode arrays (VACNF NEAs) have been explored as a sample manipulation tool and coupled with fluorescence, surface enhanced Raman scattering (SERS) and impedance techniques for pathogen detection and identification. The key objective for employing a nanoelectrode array is that the nano-Dielectrophoresis (nano-DEP) at the tip of a carbon nanofiber (CNF) acts as a potential trap to capture pathogens. A microfluidic device was fabricated where nanofibers (~ 100 nm in diameter) were placed at the bottom of a fluidic channel to serve as a ‘point array’ while an indium tin oxide coated glass slide acted as a macroscale counter electrode. The electric field gradient was highly enhanced at the tips of the CNFs when an AC voltage was applied. The first study focused on the capture of the viral particles (Bacteriophage T4r) by employing a frequency of 10.0 kHz, a flow velocity of 0.73 mm/sec, and a voltage of 10.0 Vpp. A Lithenburg type of phenomenon was observed, that were drastically different from the isolated spots of bacteria captured on VACNF tips in previous study. At the lowest employed virus concentration (1 × 10[superscript]4 pfu/mL), a capture efficiency of 60% was observed with a fluorescence microscope. The motivation of the second study was to incorporate the SERS detection for specific pathogen identification. Gold-coated iron-oxide nanoovals labeled with Raman Tags (QSY 21), and antibodies that specifically bound with E.coli cells were utilized. The optimum capture was observed at a frequency of 100.0 kHz, a flow velocity of 0.40 mm/sec, and a voltage of 10.0 Vpp. The detection limit was ~210 CFU/mL for a portable Raman system with a capture time of 50 seconds. In the final study, a real-time impedance method was employed to detect Vaccinia virus (human virus) in the nano-DEP device at 1.0 kHz and 8.0 Vpp giving a detection limit of 2.51 × 10[superscript]3 pfu/mL.

This dissertation explores the different ways to create thin film-based biosensors that are capable of rapid and label-free detection of cortisol, a non-specific biomarker closely linked to stress, within the physiological range of 10pM to 10 uM. Increased cortisol levels have been linked to stress-related diseases, such as chronic fatigue syndrome, irritable bowel syndrome, and post-traumatic stress disorder. It also plays a role in the suppression of the immune system as well. Therefore, accurate measurement of cortisol in saliva, serum, plasma, urine, sweat, and hair, is clinically significance to predict physical and mental diseases. In this dissertation, thin film-based electrochemical immunosensors were fabricated using a self-assembled monolayer (SAM) functionalized by cortisol specific antibodies to detect cortisol at 10 pM level sensitivities in the presence of a redox probe. The fabricated electrochemical cortisol immunosensors were able to detect cortisol in human saliva samples and the outcomes were validated using the standard Enzyme Linked Immuno Sorbent Assay (ELISA) technique. With the aim of improving signal amplification and label-free cortisol detection, copper nanoparticles were incorporated on screen-printed carbon electrodes (SPCE) for the fabrication of electrochemical cortisol immunosensor. This SPCE-based sensor showed a sensitivity of 4.21µA/M and the limit of detection 6.6nM. Both the SAM and SPCE-based immunosensors were not thermally stable due to the instability of antibodies at room temperature. To address this issue, an antibody-free immunosensor was fabricated. Molecular Imprinted Polymer (MIP) was used to template the target cortisol molecule. The MIP-based sensing platform was prepared using polypyrrole, a thermally stable conducting polymer. The conductivity of the polymer ensured good electrical performance. The polypyrrole-based MIP was synthesized by means of electrochemical polymerization and was used to detect cortisol within the physiological range at room temperature. MIP-based sensors exhibited the detection limit of 1 pM, and were cost-effective, easy to fabricate, temperature stable, and reusable. The sensing performance of the resulting sensors was comparable to those of commercially available technologies, such as ELISA. Aiming to perform cortisol sensing at point-of-care (POC), an Extended Gate Field Effect Transistor (EGFET) was integrated with a developed MIP cortisol sensor. The as developed MIP-EGFET sensor was used to detect the cortisol concentration in the range of 1 pM to 100 nM. A few of the major advantages of the developed sensor are its ability to provide a direct readout and simpler electronic systems, which are necessary for miniaturized Point of Care devices.

Hybrid plasmonic-photonic structures were introduced as novel platforms for on-chip biochemical sensing and spectroscopy. By appropriate coupling of photonic and plasmonic modes, a hybrid architecture was realized that can benefit from the advantages of integrated photonics such as the low propagation loss, ultra-high Q modes, and robustness, as well as the advantages of nanoplasmonics such as extreme light localization, large sensitivities, and ultra-high field enhancements to bring about unique performance advantages for efficient on-chip sensing. These structures are highly sensitive and can effectively interact with the target biological and chemical molecules. It was shown that interrogation of single plasmonic nanoparticles is possible using a hybrid waveguide and microresonator-based structure, in which light is efficiently coupled from photonic structures to the integrated plasmonic structures. The design, implementation, and experimental demonstration of hybrid plasmonic-photonic structures for lab-on-chip biochemical sensing applications were discussed. The design goal was to achieve novel, robust, highly efficient, and high-throughput devices for on-chip sensing. The sensing scenarios of interest were label-free refractive index sensing and SERS. Nanofabrication processes were developed to realize the hybrid plasmonic-photonic structures. Silicon nitride was used as the material platform to realize the integrated photonic structure, and gold was used to realize plasmonic nanostructures. Special optical characterization setups were designed and implemented to test the performance of these nanoplasmonic and nanophotonic structures. The integration of the hybrid plasmonic-photonic structures with microfluidics was also optimized and demonstrated. The hybrid plasmonic-photonic-fluidic structures were used to detect different analytes at different concentrations. A complete course of research from design, fabrication, and characterization to demonstration of sensing applications was conducted to realize nanoplasmonic and integrated photonic structures. The novel structures developed in this research can open up new potentials for biochemical sensors with advanced on-chip functionalities and enhanced performances.

In this thesis, a systematic study has been carried out on the synthesis, characterization and device fabrication of piezoelectric ZnO nanstructures. The achieved results are composed of the following four parts. Firstly, through a systematic investigation on the Sn-catalyzed ZnO nanostructure, an improved understanding of the chemical and physical process occurring during the growth of hierarchical nanostructures has been achieved. Decomposed Sn from SnO2 has been successfully demonstrated and proved to be an effective catalyst guiding the growth of not only aligned ZnO nanowires, but also the hierarchical nanowire-nanoribbon junction arrays and nanopropeller arrays. During the vapor-liquid-solid (VLS) catalyzing growth process at high temperature, Sn in the liquid state has been proved to be able to guide the growth of nanowires and nanoribbons in terms of growth directions, side facets, and crystallographic interfaces between Sn and ZnO nanostructures. Secondly, using pure ZnO as the only source material, by precisely tuning and controlling the growth kinetics, a variety of hierarchical polar surface dominated nanostructures have been achieved, such as single crystal nanorings, nanobows, nanosprings and superlattice nanohelices. High yield synthesis of ZnO nanosprings over 50% has been successfully obtained by mainly controlling the pre-pumping level associated with the partial pressure of residual oxygen during the vapor-solid growth process. The rigid superlattice nanohelices of ZnO have been discovered, which is a result of minimization of the electrostatic energy induced by polar surfaces. The formation process of the nanohelix has been systematically characterized. Thirdly, two new strategies have been successfully developed for fabricating ZnO quantum dots and synthesis of ZnO nanodiskettes and nanotubes. The formation process is based on a common concept of self-assembly. Finally, a series of devices and applications studies based on several piezoelectric ZnO nanostructures, such as nanobelts, nanopropellers and nanohelices, have been carried out utilizing the electro-mechanical resonance, bio-surface functionalization, devices fabrication and electrical characterization. Individual nanobelt and nanohelix based nanodevices have been successfully fabricated for applications in chemical and biological sensing. The study opens a few new areas in oxide nanostructures and applications.

Fluorescence lifetime determination and allied studies find application in spectroscopy in general and fiber optic biosensors in particular. Instruments and sensors cited in literature however use open loop, intensity based techniques with sophisticated detectors and components. We propose phase sensitive signal processing schemes to estimate the fluorescence lifetime using simple detectors and components, without compromising on accuracy. The performance of the schemes proposed is analysed and contrasted from a communications (signals and systems) point of view. The resolution and sensitivity limits imposed in processing the signal, by systematic errors and additive noise, are derived for the schemes suggested. It is found that systematic errors impose a phase resolution limit of about 2°. We then study the suitability of different detectors and channels for application in phase sensitive fluorescence biosensors we analyse the effect of systematic limitations as well as additive noise, in the detection/transmission process, from the point of view of the components used. Certain fundamental limits of operation in terms of excitation intensities are derived for different detector-channel combinations, with a view to obtain a given resolution. A photodiode used with a fiber bundle is found to be sufficient for accurate phase read outs with 10"4 radians resolution. A PMT used in conjunction with a multimode fiber serves as a very good device for microsensing applications Lastly, the biosensor for oxygen sensing, the ruthenium complex, is studied for standardisation of the sensor. We examine the quenching of fluorescence, the repeatability and reusability of the sensor, the stability of the instrument and such.

The present thesis work titled “Analysis and characterisation of biological samples in nano and microfluidic devices using AC and DC electric fields” has as main objective study the effects that electric fields have biologic samples to develop microfluidic tools (lab-on-a-chip) that allow to manipulate and sensing these samples. This work is divided in three main issues oriented to develop different modules for a diagnostic device. In the first block, we studied the movement of DNA molecules confined in a nanochannel of 20 nm height under the effect of DC and AC electric fields. The objective is to determine the mechanism behind the size separation of DNA molecules, in gel-free environments. The second block presents the development of a new dielectrophoretic system for size sorting of cells. It is based in the competence between dielectrophoretic forces and the dragging forces generated by the fluid motion. The system is able to separate red blood cells form monocytes in physiological conditions (high conductivity) in continuously flow. And finally, in the third block it is developed a new instrumentation for microcytometry applications based on impedance detection. The electronic device is validated by using a synchronised optical detection system that allow us relate the obtained signal with the position of the cell on the sensing area. The system demonstrated good sensing and sizing capabilities. We also used hydrodynamic focusing, to increase the sensing capabilities of a sensing geometry base don coplanar electrodes.
Esta tesis titulada “Analysis and characterisation of biological samples in nano and microfluidic devices using AC and DC electric fields” tiene como objetivo el estudiar los efectos que tienen los campos eléctricos sobre muestras biológicas con el fin de desarrollar herramientas microfluídicas (lab-on-a-chip) para la manipulación y detección de las muestras biológicas. El trabajo está dividido en tres ámbitos orientados a desarrollar dispositivos o módulos en un dispositivo para diagnóstico. En el primer bloque estudiamos el movimiento de moléculas de ADN (-DNA) en el interior de nanocanales de 20 nm de alto bajo la influencia de campos DC y AC. El objetivo es determinar el mecanismo que hay detrás de la separación por tamaño de esta molécula en ausencia de geles y matrices. En el segundo bloque desarrollamos un nuevo sistema dielectroforético de separación celular por tamaño, basado en la competencia entre la fuerza dielectroforética y las fuerzas fluídicas de arrastre. El sistema se utiliza para separar glóbulos rojos de monocitos en condiciones fisiológicas (alta conductividad) y en flujo continuo. En el tercer bloque desarrollamos una instrumentación para un microcitómetro de flujo basado en medidas de impedancia. El sistema electrónico se valida mediante la utilización de un sistema de óptico sincronizado que nos permite relacionar la señal obtenida con el paso de las células sobre el área de detección. Mediante este sistema se ponen aprueba las capacidades de detección, así como la capacidad de distinguir células por tamaño. Finalmente utilizamos el efecto de la focalización hidrodinámica para mejorar las prestaciones de sensibilidad de un sistema de electrodos coplanares.

The analysis and development of robust sensing platforms based on solidly-mounted ZnO bulk acoustic wave devices was proposed. The exploitation of acoustic energy trapping was investigated and demonstrated as a method to define active sensing areas on a substrate. In addition, a new "hybrid" acoustic mode experiencing acoustic energy trapping was studied theoretically and experimentally. This mode was used as an explanation of historical inconsistencies in observed thickness-shear mode velocities. Initial theoretical and experimental results suggest that this mode is a coupling of thickness-shear and longitudinal particle displacements and, as such, may offer more mechanical and/or structural information about a sample under test. Device development was taken another step further and multi-mode ZnO resonators operating in the thickness-shear, hybrid, and longitudinal modes were introduced. These devices were characterized with respect to sample viscosity and conductivity and preliminary results show that, with further development, the multi-mode resonators provide significantly more information about a sample than their single-mode counterparts. An alternative to resonator-based platforms was also presented in the form of bulk acoustic delay lines. Initial conceptual and simulation results show that these devices provide a different perspective of typical sensing modalities by using properly designed input pulses, device tuning, and examining overall input and output signal spectra.

Dans la lignée des progrès technologiques récents en électronique, ces dernières décennies ont vu l’émergence d’une variété de systèmes permettant l’interface bioélectronique, allant de la mesure de l’activité électrique émise par l’ensemble du cerveau jusqu’à la mesure du signal émis par un neurone unique. Bien que des interfaces électroniques avec les neurones ont montré leur utilité pour des applications cliniques et sont communément utilisés par les neurosciences fondamentales, leurs performances sont encore très limitées, notamment en raison de l’incompatibilité relative entre les systèmes à l’état solide et le vivant. Dans ce travail de thèse, nous avons étudié des techniques et des matériaux nouveaux permettant une approche alternative et qui pourraient améliorer le suivi de l’activité de réseaux de neurones cultivés in situ et à terme la performance des neuroprothèses in vivo. Dans ce travail, des réseaux de nanofils de silicium et des microélectrodes en diamant sont élaborés pour respectivement améliorer la résolution spatiale et la stabilité des électrodes dans un environnement biologique. Un point important de cette thèse est également l’évaluation des performances de transistors à effet de champ en graphène pour la bio électronique. En raison des performances remarquables et combinées sur les aspects électrique, mécanique et chimique du graphène, ce matériau apparaît comme un candidat très prometteur pour la réalisation d’une électronique permettant une interface stable et sensible avec un réseau de neurones. Nous montrons dans ce travail l’affinité exceptionnelle des neurones avec une surface de graphène brut et la réalisation d’une électronique de détection rapide et sensible à base de transistor en graphène
In line with the technological progress of last decades a variety of adapted bioelectrical interfaces was developed to record electrical activity from the nervous system reaching from whole brain activity to single neuron signaling. Although neural interfaces have reached clinical utility and are commonly used in fundamental neuroscience, their performance is still limited. In this work we investigated alternative materials and techniques, which could improve the monitoring of neuronal activity of cultured networks, and the long-term performance of prospective neuroprosthetics. While silicon nanowire transistor arrays and diamond based microelectrodes are proposed for improving the spatial resolution and the electrode stability in biological environment respectively, the main focus of this thesis is set on the evaluation of graphene based field effect transistor arrays for bioelectronics. Due to its outstanding electrical, mechanical and chemical properties graphene appears as a promising candidate for the realization of chemically stable flexible electronics required for long-term neural interfacing. Here we demonstrate the outstanding neural affinity of pristine graphene and the realization of highly sensitive fast graphene transistors for neural interfaces

De nos jours, le domaine biomédical est en pleine croissance avec le développement de dispositifs thérapeutiques innovants, bas coût, pour le diagnostic, le traitement ou la prévention de maladies chroniques ou cardiovasculaires. Ces dernières années ont connu l’émergence des polymères semi-conducteurs, alternative intéressante aux matériaux inorganiques, présentant des propriétés uniques de conduction ionique et électronique. Tout d’abord, j’ai axé mes travaux de recherche sur le développement et l’optimisation d’une encre conductrice à base de PEDOT:PSS, parfait candidat comme matériau, pour la transduction des signaux biologiques en signaux électriques, compatible avec le process jet d’encre, pour la réalisation de dispositifs imprimés. Puis mes travaux se sont orientés vers la conception et l’étude d’électrodes imprimées sur supports papiers, tatous et textiles permettant des enregistrements long termes d’électrocardiogrammes (ECG) ou électromyogrammes (EMG), présentant des performances similaires aux électrodes commerciales, utilisant un système d’acquisition spécifique pour la mesure d’activités électriques de tissus musculaires. Puis dans un second temps, je me suis penchée sur l’impression sur support papier, de transistors organiques électrochimiques (OECTs) fonctionnalisés, afin de permettre la détection d’éléments biologiques ou chimiques comme l’alcool. Ces travaux proposent une nouvelle voie pour la conception de dispositifs innovants biomédicaux à bas couts, imprimés, permettant la personnalisation des produits pouvant être intégrés dans des dispositifs biomédicaux portables ou dans des vêtements « intelligents »
With the evolution of microelectronics industry and their direct implementation in the biomedical arena, innovative tools and technologies have come to the fore enabling more reliable and cost-effective treatment. In this thesis I focus on the integration of the conducting polymer PEDOT:PSS with printing technologies toward the realization of performant biomedical devices. In the first part, I focus on the optimization of the conducting ink formulation. Following, I emphasize on the fabrication of inkjet printed PEDOT:PSS based biopotential electrodes on a wide variety of substrates (i.e., paper, textiles, tattoo paper) for use in electrophysiological applications such as electrocardiography (ECG) and electromyography (EMG). Printed electrodes on paper and printed wearable electrodes were fabricated and investigated for long-term ECG recordings. Then, conformable printed tattoo electrodes were fabricated to detect the biceps activity during muscle contraction and the conventional wiring was replaced by a simple contact between the tattoo and a similarly ink-jet printed textile electrode.In the last part, I present the potentiality of inkjet printing method for the realization of organic electrochemical transistor (OECTs) as high performing biomedical devices. A disposable breathalyzer comprised of a printed OECT and modified with alcohol dehydrogenase was used for the direct alcohol detection in breath, enabling future integration with wearable devices for real-time health monitoring. Their compatibility with printing technologies allows the realization of low-cost and large area electronic devices, toward next-generation fully integrated smart biomedical devices

La prevenció i el control de les malalties transmissibles depenen, en gran mesura, de la detecció ràpida i eficaç. Els mètodes convencionals per a la detecció d'un patogen, com ara el cultiu microbiològic, generalment requereixen molt de temps, són laboriosos, necessiten personal qualificat i no són aptes com a eines de diagnòstic en el punt d'atenció. El desenvolupament de mètodes de diagnòstic ràpid en el marc dels criteris ASSURED, de l'anglès (A) Affordable, (SS) Sensitive i Didàctiques, (O) User-friendly, (R) Rapid and Robust, (I) Equipment free, and (d) Deliverable to those who need it, Affordable, descrits per l'Organització Mundial de la Salut (OMS), es troben en l'actualitat sota intens estudi. Per tant, la present tesi aborda el disseny i desenvolupament d'estratègies, mètodes i materials per millorar les prestacions analítiques i simplificar el procediment en proves de diagnòstic ràpid, incloses noves estratègies de preconcentració en fase sòlida, mètodes d'amplificació i materials avançats, així com la seva integració en diferents plataformes (principalment biosensors basats en detecció electroquímica i proves en paper amb lectura òptica). En tots els casos, les aplicacions seleccionades es centren en malalties transmissibles, inclosos els patògens transmesos pels aliments i els micobacteris. Amb aquesta finalitat, es comparen dues plataformes basades en paper en diferents configuracions (flux lateral i vertical) en termes de rendiment analític per a la detecció de Mycobacterium. Per aconseguir una millora addicional en el límit de detecció, s'estudia la preconcentració prèvia dels bacteris per separació immunomagnètica. En segon lloc, s'avaluen i es comparen en termes del seu rendiment analític la detecció simultània de Salmonella i E. coli mitjançant flux lateral d'àcid nucleic amb lectura visual i genosensors electroquímics. Si bé aquests mètodes requereixen PCR de doble etiquetatge per a l'amplificació, es poden adaptar fàcilment a termocicladors portàtils que funcionen amb bateries per poder ser realitzats en entorns amb recursos limitats per satisfer les demandes de diagnòstic ASSURED. A més, també es presenta en aquesta tesi la síntesi de polímers magnètics impresos molecularment, per tal de reemplaçar les partícules magnètiques biològicament modificades, i prenent com a model la detecció de biotina i de molècules biotinilades. A més, es realitza la caracterització del material mitjançant diferents tècniques analítiques i es compara, en tots els casos, amb el polímer no imprès. Aquest material biomimètic mostra un gran potencial per a la preconcentració i detecció d'una àmplia gamma d'analits. Malgrat tot els progressos, les tècniques d'amplificació d'àcid nucleic segueixen essent necessàries per assolir els límits de detecció requerits en algunes malalties transmissibles. En aquest sentit, les tècniques d'amplificació isotèrmiques són bons candidats per dur a terme proves de diagnòstic en entorns on la PCR pot ser una barrera. En concret, es descriu en aquest treball la detecció d' E.coli mitjançant un genosensor electroquímic basat en l'amplificació isotèrmica. En aquest cas, s'optimitza la lectura electroquímica per voltamperometria d'ona quadrada en elèctrodes d'un sol ús comparant dues estratègies de marcatge del producte amplificat. És important ressaltar que totes aquestes estratègies apunten a ser utilitzades com a eines per millorar les proves de diagnòstic ràpid en entorns de baixos recursos, per interrompre la cadena d'infecció de malalties transmissibles i permetre, per tant, un tractament precoç.
La prevención y el control de las enfermedades transmisibles dependen, en gran medida, de la detección rápida y eficaz. Los métodos convencionales para la detección de un patógeno, como el cultivo microbiológico, generalmente requieren mucho tiempo, son laboriosos, necesitan personal cualificado y no son aptos como herramientas de diagnóstico en el punto de atención. El desarrollo de métodos de diagnóstico rápido en el marco de los criterios ASSURED, del inglés (A) Affordable, (SS) Sensitive and Specific, (U) User-friendly, (R) Rapid and Robust, (E) Equipment free, and (D) Deliverable to those who need it, Affordable, descritos por la Organización Mundial de la Salud (OMS), se encuentran en la actualidad bajo intenso estudio. Por lo tanto, la presente tesis aborda el diseño y desarrollo de estrategias, métodos y materiales para mejorar las prestaciones analíticas y simplificar el procedimiento en pruebas de diagnóstico rápido, incluidas nuevas estrategias de preconcentración en fase sólida, métodos de amplificación y materiales avanzados, así como su integración en diferentes plataformas (principalmente biosensores basados en detección electroquímica y pruebas en papel con lectura óptica). En todos los casos, las aplicaciones seleccionadas se centran en enfermedades transmisibles, incluidos los patógenos transmitidas por los alimentos y las micobacterias. Con este fin, se comparan dos plataformas basadas en papel en diferentes configuraciones (flujo lateral y vertical) en términos del rendimiento analítico para la detección de Mycobacterium. Para lograr una mejora adicional en el límite de detección, se estudia la preconcentración previa de las bacterias por separación inmunomagnética. En segundo lugar, se evalúan y se comparan en términos de su rendimiento analítico la detección simultánea de Salmonella y E. coli mediante flujo lateral de ácido nucleico con lectura visual y genosensores electroquímicos. Si bien estos métodos requieren PCR de doble etiquetado para la amplificación, se pueden adaptar fácilmente a termocicladores portátiles que funcionan con baterías para poder ser realizados en entornos con recursos limitados para satisfacer las demandas de diagnóstico ASSURED. Además, también se presenta en esta disertación la síntesis de polímeros magnéticos impresos molecularmente, con el objeto de reemplazar las partículas magnéticas biológicamente modificadas, y tomando como modelo la detección de biotina y moléculas biotiniladas. Además, se realiza la caracterización del material mediante diferentes técnicas analíticas y se compara, en todos los casos, con el polímero no impreso. Este material biomimético muestra un gran potencial para la preconcentración y detección de una amplia gama de analitos. A pesar de todo este progreso, las técnicas de amplificación de ácido nucleico siguen siendo necesarias para alcanzar los límites de detección requeridos en algunas enfermedades transmisibles. Las técnicas de amplificación isotérmica son buenos candidatos para llevar pruebas de diagnóstico en entornos donde la PCR puede ser una barrera. En concreto, se describe en esta disertación la detección de E. coli mediante un genosensor electroquímico basada en la amplificación isotérmica. En este caso, se optimiza la lectura electroquímica por voltamperometría de onda cuadrada en electrodos desechables comparando dos estrategias de marcaje del producto amplificado. Es importante resaltar que todas estas estrategias apuntan a ser utilizadas como herramientas para mejorar las pruebas de diagnóstico rápido en entornos de bajos recursos, para interrumpir la cadena de infección de enfermedades transmisibles y permitir, por tanto, un tratamiento precoz.
The prevention and control of communicable disease rely, to a large extent, on effective and early detection approaches. Conventional methods for the detection of a pathogen, such as microbiological culture, are usually time-consuming, laborious, need skilled personnel and are non-amenable to point-of-care diagnostic tools. The development of rapid diagnostic methods in the framework of the ASSURED criteria as (A) Affordable, (SS) Sensitive and Specific, (U) User-friendly, (R) Rapid and Robust, (E) Equipment free, and (D) Deliverable to those who need it, outlined by the World Health Organization (WHO), are under intensive study. Therefore, the present dissertation addresses the design and development of strategies, methods and materials to improve the analytical performance and to simplify the analytical procedure in rapid diagnostic tests, including novel solid-phase preconcentration strategies, amplification methods and advanced materials, as well as their integration in different platforms (mainly biosensors based on electrochemical detection and paper-based strips for optical readout). In all instances, the applications selected are focused on communicable diseases, including foodborne pathogens and mycobacteria. Therefore, two paper-based platforms in different configurations (nucleic acid lateral and vertical flow) are compared in terms of the analytical performance for the detection of Mycobacterium. In order to achieve a further improvement in the limit of detection, the preconcentration of the bacteria is performed by immunomagnetic separation. Secondly, the simultaneous detection of Salmonella and E. coli by nucleic acid lateral flow with visual readout and electrochemical genosensing are evaluated and compared in terms of their analytical performance. Although these methods required double-tagging PCR for amplification, portable, battery-powered thermocyclers can easily be adapted for resource-constrained settings to meet the demands for ASSURED diagnosis. Furthermore, the synthesis of Magnetic Molecularly Imprinted Polymers, in order to replace biological-modified magnetic particles is also presented in this dissertation, taking as a model the detection of biotin and biotinylated molecules with outstanding performance. Moreover, the characterization of the material is performed by different analytical techniques and compared, in all instances, with the non-imprinted polymer. This biomimetic material shows a great potential for the preconcentration and detection of a huge range of analytes. Despite all these progress, nucleic acid amplification techniques are still necessary to reach the challenging limits of detection required in some communicable disease. Isothermal amplification techniques are good candidates to bring sensitive diagnostic tests in places where the PCR can be a barrier. In detail, the electrochemical genosensing of E. coli based on isothermal amplification is also described in this dissertation. In this approach, the electrochemical readout by square-wave voltammetry on disposable electrodes is optimized comparing two different labelling approaches. It is important to highlight that all these strategies aim to be used as tools for the improvement of rapid diagnostic test in low resource settings, to interrupt the chain of infection of communicable diseases and enabling the rapid treatment.

Esta tesis doctoral resume el trabajo realizado en el Departamento de Electrónica de la Facultad de Física, en la Universidad de Barcelona. El objetivo de la misma se centra en el diseño y fabricación de un microsistema óptico basado en la integración híbrida de componentes comerciales y procesos de micromecanizado en silicio, destinado a la detección óptica de micropartículas en chips de microfluídica. Todo ello teniendo como principales metas la miniaturización y la integración de todos los componentes para obtener un sistema robusto, portátil, orientado a aplicaciones “Point of care”. El sistema de detección óptica de partículas incluye dos elementos comerciales. Por una parte, las fuentes de luz escogidas, láseres VCSEL en formato “die” de la empresa ULM Photonics, y por otra, una matriz de microlentes fabricada por SUSS microOptics. La matriz de microlentes se adapta al pitch que existe entre láseres es de 250 micras, cosa que la hace totalmente compatible en términos de alineación óptica. Para determinar las posiciones óptimas de estos componentes, se realiza el estudio de dos escenarios mediante el uso de un simulador de trazado de rayos (ZEMAX Radiance ®): el primero, basado en la obtención de haces de luz colimados; el segundo, basado en la obtención de haces de luz focalizados. Los componentes comerciales se ensamblan en una estructura robusta, formada por dos piezas de silicio (base y separador óptico), y con alienación pasiva de las microlentes. Las piezas de silicio se fabrican en obleas siguiendo procesos de Sala Blanca. Mediante técnicas de soft lithography se diseñan y fabrican diversos chips para el bloque de microfluídica: canales con focalización pasiva del flujo y canales con sistemas de focalización activa. Dichos chips contienen los canales de microfluídica por donde circularán las partículas que se pretende detectar, en suspensión líquida. El sistema de detección óptica de partículas requiere de un sensor óptico encargado de detectar las variaciones en los niveles de intensidad luminosa causadas por la circulación de partículas. En esta tesis se plantea un sensor de imagen basado en tecnología CMOS, con un diseño full-custom. El sensor contiene una estructura en doble array lineal con 256 pixels. Para validar la funcionalidad del sistema fabricado, se realizó una batería de pruebas. Se prepararon diversas suspensiones acuosas en agua desionizada e isopropanol con partículas de diferentes tamaños (diámetros), materiales y fabricantes en un rango de 10 a 90micras de diámetro. Los resultados fueron satisfactorios en todos los casos.
This thesis summarizes the work developed in the Department of Electronics, Faculty of Physics, at the University of Barcelona. This work is focused on the design and fabrication of an optical microsystem based on hybrid integration of commercial components and silicon micromachining processes, in order to the optical detection of microparticles in microfluidic chips. Main goals are the miniaturization and integration of all components to obtain a robust system, portable, and oriented to "Point of care" applications. The optical detection system includes two commercial components. First, the chosen light sources, VCSEL lasers in "die " format from ULM Photonics, and second, an array of microlenses manufactured by SUSS microoptics. The microlens array fits the existing pitch between lasers (250 microns), therefore it is fully compatible in terms of optical alignment. To determine the optimal positions of these components, two scenarios are analyzed by using a ray tracing simulator (ZEMAX Radiance ®): the first, based on collimated light beams, the second based on obtaining focused light beams. The commercial components are assembled in a robust structure, consisting of two pieces of silicon (base and optical spacer), and passive alignment of the microlenses. The pieces of silicon are fabricated in wafers at the clean room of the IBM-CNM, according to the defined processes. Using soft lithography techniques, various chips for the microfluidic block are designed and fabricated: passive focusing channels and channels with hydrodynamic focusing. These chips contain microfluidic channels where particles to be detected will flow in liquid suspension. The optical detection system requires an optical sensor to detect the variations in the levels of light intensity caused by the particles circulation. In this thesis, an image sensor based on CMOS technology and a full-custom design is presented. The sensor includes a double linear array structure with 256 pixels and other electronics. To validate the functionality of the proposed system, we performed a battery of tests. Several aqueous suspensions were prepared in deionized water and isopropanol with particles of different sizes (diameters) materials and manufacturers in the range of 10 to 90micras diameter. The results were satisfactory in all cases.

Biosensors are today important devices within various application areas. In this thesis a new type of label-free biosensor device is studied, which is fabricated using the same processes used for the fabrication of integrated circuits. This enables tighter integration and further sensors/biosensor miniaturization. The device is a so-called Thin Film Bulk Acoustic Resonator (FBAR). Within this thesis a low temperature reactive sputtering process for growing AlN thin films with a c-axis inclination of 20-30o has been developed. This enables shear mode FBAR fabrication suitable for in-liquid operation, essential for biosensor applications. Shear mode FBARs were fabricated operating at frequencies above 1GHz exhibiting Q values of 100-200 in water and electromechanical coupling factors kt2 of about 1.8%. This made it possible to move the thickness excited shear mode sensing of biological layers into a new sensing regime using substantially higher operation frequencies than the conventionally used quartz crystal microbalance (QCM) operating at 5-20MHz. Measured noise levels of shear mode FBARs in contact with water showed the resolution to be in the range 0.3ng/cm2 to 7.5ng/cm2. This demonstrated the FBAR resolution without any averaging or additional stabilization measures already to be in the same range as the conventional QCM (5ng/cm2), suggesting that FBARs may be a competitive and low cost alternative to QCM. The linear thickness limit for sensing of biomolecular layers was concluded to be larger than the thickness of the majority of the molecular systems envisaged for FBAR biosensor applications. A temperature compensated shear mode FBAR composite structure was demonstrated with retained coupling factor and Q-value by utilizing the second mode of operation. Understanding has been gained on the sensor operation as well as on how the design parameters influence its performance. Specifically, sensitivity amplification utilizing low acoustic impedance layers in the FBAR structure has been demonstrated and explained. Further, temperature compensated Lamb mode (FPAR) devices were also studied and demonstrated with optimized electromechanical couplings.
wisenet

A biosensor is an analytical device integrating a biological element and a physicochemical transducer that convert a biological response into a measurable signal. The advantages of biosensors include low cost, small size, quick, sensitivity and selectivity greater than the conventional instruments. Biosensors have a wide range of applications ranging from clinical diagnostics through to environmental monitoring, agriculture industry, et al. The different types of biosensors are classified based on the sensor device as well as the biological material. Biosensors can be broadly classified into (piezoelectric, etc.), electrochemical biosensors (potentiometric, amperometric, etc.), and optical types of biosensors (fiber optics, etc.). Here, we introduce a novel microfluidics-integrated biosensor platform system that can be flexibly adapted to form individual biosensors for different applications. In this dissertation, we present five examples of different emerging areas with this biosensor system including anti-cancer drug screening, glucose monitoring, heavy metal elements measurement, obesity healthcare, and waterborne pathogen DNA detection. These micro-biosensors have great potential to be further developed to emerging portable sensing devices especially for the uses in the developing and undeveloped world. At the last chapter, Raman spectroscopy applied to assess gestational status and the potential for pregnancy complications is presented and discussed. This technique could significantly benefit animal reproduction.

Schistosomiasis is a parasitic disease affecting over 200 million people worldwide. This study reports the design and development of a microfiltration device for isolating schistosome eggs in urine for rapid diagnostics of urogenital schistosomiasis. The design of the device comprises a linear array of microfluidic traps to immobilize and separate schistosome eggs. Sequential loading of individual eggs is achieved autonomously by flow resistance, which facilitates observation and enumeration of samples with low-abundance targets. Computational fluid dynamics modeling and experimental characterization are performed to optimize the trapping performance. By optimizing the capture strategy, the trapping efficiency could be achieved at 100% with 300 mu l/min and 83% with 3000 mu l/min, and the filtration procedure could be finished within 10 min. The trapped eggs can be either recovered for downstream analysis or preserved in situ for whole-mount staining. On-chip phenotyping using confocal laser fluorescence microscopy identifies the microstructure of the trapped schistosome eggs. The device provides a novel microfluidic approach for trapping, counting and on-chip fluorescence characterization of urinal Schistosoma haematobium eggs for clinical and investigative application.

PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO
COORDENAÇÃO DE APERFEIÇOAMENTO DO PESSOAL DE ENSINO SUPERIOR
CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO
PROGRAMA DE SUPORTE À PÓS-GRADUAÇÃO DE INSTS. DE ENSINO
O presente trabalho investiga a utilização de fibras ópticas em biossensoriamento e na indução de uma não-linearidade de segunda ordem para a construção de dispositivos sensores. O biossensor proposto tem por finalidade diagnosticar uma das doenças com maior incidência em países tropicais: a Dengue. Foi construído um sensor a fibra óptica que potencialmente é capaz de diagnosticar, num tempo curto, a presença do vírus da Dengue no sangue de um paciente infectado. Esse sensor usa nanopartículas de ouro, depositadas na extremidade de uma fibra óptica, que foram funcionalizadas com os anticorpos da Dengue (anti-NS1). O sensor é capaz de detectar o antígeno NS1 em diferentes concentrações com um limite de quantificação de 0.074 micrograma por mililitro, podendo ser explorado para uso na fase aguda da infecção.Outra vertente do trabalho é a possibilidade de se realizar modificações estruturais nas fibras ópticas com o intuito de alterar as propriedades ópticas da fibra. Através da técnica de polarização térmica, é possível gravar campos elétricos da ordem de 108 volts por metro no núcleo da fibra óptica, sendo possível utilizar as fibras polarizadas como moduladores de fase e de amplitude, seletores de pulso, chaves ópticas, voltímetros, entre outras. O trabalho de tese aqui descrito apresenta um estudo detalhado da polarização térmica em fibras ópticas através de simulações, utilizando o software COMSOL Multiphysics, considerando-se os diversos parâmetros envolvidos e geometrias diferentes de fibras, visando a obtenção de uma alta não-linearidade de segunda ordem. Além do mais, experimentos foram realizados a fim de se entender o mecanismo presente no processo de polarização térmica face aos resultados obtidos pela simulação. Buscou-se, também, entender o papel dos portadores de cargas presentes no material no processo de geração de não-linearidade de segunda ordem realizando-se experimentos de polarização óptica.
The present work investigates the use of fiber optics in biosensing and the creation of a second order nonlinearity to be use in the development of sensor devices. The goal of the proposed biosensor is to diagnose one of the diseases with highest incidence in tropical countries: Dengue. Dengue is a dangerous disease that every year affects more and more people, despite the efforts made to deal with the transmitter, the mosquito Aedes aegypti. Furthermore, since Dengue symptoms resemble flu symptoms, wrong diagnoses are frequently made. As a consequence, wrong medicines may be prescribed, and that may lead the patient to death. Another problem in diagnosing Dengue is the long time is necessary for the laboratorial exams to give a result. In an attempt to offer a solution that could minimize these problems, an LSPR-based fiber optic sensor was adapted for antigen NS1 detection. This sensor is potentially able to perform a Dengue s virus diagnosis in a short period of time in an infected patient s blood. It uses gold nanoparticles that are functionalized with Dengue s antibodies. The antibody, anti-NS1, was immobilized in gold nanoparticles deposited at the endface of a multimode optical fiber. The LSPR sensor is able to detect different concentrations of the antigen NS1 with a limit of quantification equal to 0.074 microgram per milliliter, and may be used in the acute phase of the infection. Another part of the present work investigates the possibility of performing structural modifications in the optical fiber to change the optical properties of silica. Through the electro-thermal poling technique it is possible to record electric fields as high as 108 volts per meter in the core of the fiber, making possible the use of these modified fibers as phase and amplitude modulators, optical keys, pulse selectors, voltmeters, etc. This work also shows a very detailed study of electro-thermal poling in optical fiber through simulations, using the software Comsol Multiphysics, considering various parameters that are involved in the process in order to obtain high second order nonlinearity. Furthermore, experiments on eletro-optical poling were performed to investigate the mechanism involved in this poling process, in order to understand the role of the carriers present in the material in the generation of the second order nonlinearity.

Point-of-care (POC) diagnostics presents a giant market opportunity with profound societal impact. In particular, specific detection of DNA and protein markers can be essential for early diagnosis of e.g. cancer, cardiovascular disease, infections or allergies. Today, identification of these markers often requires extensive laboratory work and hence is expensive and time consuming. Current methods for recognition and detection of specific biomolecules are mostly optics based and thus impose severe limitations as to convenience, specificity, sensitivity, parallel processing and cost reduction. Electronic sensors based on silicon nanowire field-effect transistors have been reported to be able to detect biomolecules with concentrations down to femtomolar (fM) level with high specificity. Although the reported capability needs further confirmation, the CMOS-compatible fabrication process of such sensors allows for low cost production and high density integration, which are favorable for POC applications. This thesis mainly focuses on the development of a multiplex detection platform based on silicon nanowire field-effect sensors integrated with a microfluidic system for liquid sample delivery. Extensive work was dedicated to developing a top-down fabrication process of the sensors as well as an effective passivation scheme. The operation mechanism and coupling efficiencies of different gate configurations were studied experimentally with the assistance of numerical simulation and equivalent circuits. Using pH sensing as a model system, large effort was devoted to identifying sources for false responses resulting from the instability of the inert-metal gate electrode. In addition, the drift mechanism of the sensor operating in electrolyte was addressed and a calibration model was proposed. Furthermore, protein detection experiments were performed using small-sized Affibody molecules as receptors on the gate insulator to tackle the Debye screening issue. Preliminary results showed that the directionality of the current changes in the sensors was in good agreement with the charge polarities of the proteins. Finally, a graphene-based capacitor was examined as an alternative to the nanowire device for field-effect ion sensing. Our initial attempts showed some attractive features of the capacitor sensor.

Le développement de systèmes de diodétection est extrêmement important pour un grand nombre de domaines et la nécessité d’amélioré la sensibilité et la précision des mesures devient un enjeu important pour certaines applications de pointe. Les ondes acoustiques de surface (SAW) sont largement utilisées pour des applications capteurs notamment pour la biodétection, cependant les limites théoriques de leur sensibilité seront bientôt atteintes. Parallèlement, de nouvelles méthodes de manipulation des ondes acoustiques grâce à des arrangements périodiques, appelés cristaux phononiques, ont été développées. L'objectif est de montrer une preuve de concept de l’interaction de structures phononiques couplées à un dispositif SAW à ondes de Love ainsi que leur sensibilité à un dépôt de masse afin de montrer leur potentiel pour des applications de biodétection. Le travail a consisté en une étape de modélisation numérique afin de concevoir et optimiser une structure phononique de référence, puis en une phase expérimentale avec le développement de processus de fabrication en salle blanche et de tests afin de caractériser les dispositifs et d’estimer une première sensibilité pour ce type de systèmes
The development of diodetection systems is extremely important for a large number of fields and the need to improve the sensitivity and precision of measurements is becoming an important issue for some advanced applications. Surface acoustic waves (SAW) are widely used for sensor applications, particularly for biodetection, however the theoretical limits of their sensitivity will soon be reached. At the same time, new methods of manipulating acoustic waves through periodic arrangements, called phononic crystals, have been developed. The objective is to show a proof of concept of the interaction of phononic structures coupled to a SAW Love waves device as well as their sensitivity to mass deposition in order to show their potential for biodetection applications. The work consisted of a numerical modeling step in order to design and optimize a reference phononic structure, then in an experimental phase with the development of cleanroom manufacturing processes and tests to characterize the devices and estimate a first sensitivity for this type of system

Microfluidic biosensors and bioreactors based on immobilized biomaterials are described in this dissertation. Photocrosslinkable hydrogel or polymeric microbeads were used as a supporting matrix for immobilizing E.coli or enzymes in a microfluidic device. This dissertation covers a microfluidic bioreactor based on hydrogel-entrapped E.coli, a microfluidic biosensor based on an array of hydrogel-entrapped enzymes, and a microfluidic bioreactor based on microbead-immobilized enzymes. Hydrogel micropatches containing E.coli were fabricated within a microfluidic channel by in-situ photopolymerization. The cells were viable in the hydrogel micropatch and their membranes could be porated by lysating agents. Entrapment of viable cells within hydrogels, followed by lysis, could provide a convenient means for preparing biocatalysts without the need for enzyme extraction and purification. Our results suggested that hydrogel-entrapped cells, immobilized within microfluidic channels, can act as sensors for small molecules and as bioreactors for carrying out reactions. A microfluidic biosensor based on an array of hydrogel-entrapped enzymes could be used to simultaneously detect different concentrations of the same analyte or multiple analyte in real time. The concentration of an enzyme inhibitor could be quantified using the same basic approach. Isolations of the microchannels within different microfluidic channels could eliminate the possibility of cross talk between enzymes. Finally, we characterized microfluidic bioreactors packed with microbead-immobilized enzymes that can carry out sequential, two-step enzyme-catalyzed reactions under flow conditions. The overall efficiency of the reactors depended on the spatial relationship of the two enzymes immobilized on the beads. Digital simulations confirmed the experimental results.

Actualment el diagnòstic de Tuberculosi (TB) es realitza en laboratoris centralitzats, emprant equips voluminosos, reactius complexos i personal capacitat, augmentant els costos i el temps per obtenir els resultats. Per aquesta raó, l’objectiu d’aquesta tesi doctoral és el desenvolupament d’una plataforma point-of-care (POC) capaç d’oferir una resposta ràpida i fiable en el diagnòstic de TB. Per dur a terme aquest objectiu, la plataforma POC integra un nou sensor fotònic incorporat en un cartutx de micofluídica d’un sol ús. El sensor fotònic consisteix en un conjunt de interferòmetres Mach-Zehnder que ofereixen una alta sensibilitat. En primer lloc, es va dur a terme una caracterització òptica per estudiar el rendiment de la plataforma POC i la seva capacitat per a ser emprada en aplicacions biosensoras. Un cop caracteritzada òpticament, es van avaluar diferents estratègies de biofuncionalització per incorporar anticossos específics com a bioreceptors a la superfície del sensor. Després d’un estudi en profunditat, es va seleccionar i es va emprar l’estratègia de biofuncionalització òptima per l’anàlisi dels biomarcadors de TB. Els biomarcadors de TB es van avaluar tant en solució tampó com en mostres biològiques, particularment en orina humana. El biomarcador més prometedor i conegut de TB és el lipoarabinomanan (LAM), un component de la paret cel·lular bacteriana. En concret, la detecció d’aquest biomarcador va ser validada amb mostres clíniques de pacients amb TB i donants sans, mostrant la capacitat de la nostra plataforma POC per discriminar aquells pacients amb tuberculosi activa. A més, el disseny del sensor fotònic permet la detecció simultània de sis biomarcadors diferents. Tenint en compte això, hem dut a terme una prova de concepte de l’ús de la plataforma biosensora POC per a la detecció d’un panell de biomarcadors de TB utilitzant nanolitografía Dip-Pen per a la deposició de cada bioreceptor en cada sensor. Els nostres resultats, validats en estudis clínics més amplis, podrien tenir importants implicacions diagnòstiques. A més, el nostre biosensor POC ofereix una sèrie d’avantatges en comparació amb els mètodes recomanats per l’Organització Mundial de la Salut.
Actualmente el diagnóstico de Tuberculosis (TB) se realiza en laboratorios centralizados, empleando equipos voluminosos, reactivos complejos y personal capacitado, aumentando los costes y el tiempo para obtener los resultados. Por esta razón, el objetivo de esta Tesis Doctoral es el desarrollo de una plataforma point-of-care (POC) capaz de ofrecer una respuesta rápida y fiable en el diagnóstico de TB. Para llevar a cabo este objetivo, la plataforma POC integra un novedoso sensor fotónico incorporado en un cartucho de micofluídica desechable. El sensor fotónico consiste en un conjunto de interferómetros Mach-Zehnder que ofrecen una alta sensibilidad. En primer lugar, se llevó a cabo una caracterización óptica para estudiar el rendimiento de la plataforma POC y su capacidad para ser empleada en aplicaciones biosensoras. Una vez caracterizada ópticamente, se evaluaron distintas estrategias de biofuncionalización para incorporar anticuerpos específicos como bioreceptores a la superficie del sensor. Después de un estudio en profundidad, se seleccionó y empleó la estrategia de biofuncionalización óptima para el análisis de los biomarcadores de TB. Los biomarcadores de TB se evaluaron tanto en solución tampón como en muestras biológicas, particularmente en orina humana. El biomarcador más prometedor y conocido de TB es el lipoarabinomanano (LAM), un componente de la pared celular bacteriana. En concreto, la detección de este biomarcador fue validada con muestras clínicas de pacientes con TB y donantes sanos, mostrando la capacidad de nuestra plataforma POC para discriminar a aquellos pacientes con Tuberculosis activa. Además, el diseño del sensor fotónico permite la detección simultánea de seis biomarcadores distintos. Teniendo esto en cuenta, hemos llevado a cabo una prueba de concepto del empleo de la plataforma biosensora POC para la detección de un panel de biomarcadores de TB utilizando nanolitografía Dip-Pen para la deposición de cada bioreceptor en cada sensor. Nuestros resultados, validados en estudios clínicos más amplios, podrían tener importantes implicaciones diagnósticas. Además, nuestro biosensor POC ofrece una serie de ventajas en comparación con los métodos recomendados por la Organización Mundial de la Salud.
Nowadays, Tuberculosis (TB) diagnosis is carried out at centralised laboratories, employing bulky equipment, complex reagents, and trained staff, increasing costs and the time to obtain the results. For that reason, the aim of this Doctoral Thesis is to develop a point-of-care (POC) platform able to deliver a prompt and reliable response to TB diagnosis, taking advantage of a highly sensitive evanescent wave optical sensor. The POC platform integrates a novel photonic sensor consisting of a Mach-Zehnder Interferometer transducer array incorporated in a disposable microfluidic cartridge. Firstly, an optical characterisation was carried out to study the new POC performance and its ability to be employed for biosensing applications. Once the POC platform was optically characterised, diverse biofunctionalisation strategies were tested in order to incorporate specific antibodies as bioreceptors to the sensor surface. After an in-depth study, the optimal biofunctionalisation strategy was selected and employed for the analysis of the TB biomarkers. The TB biomarkers were evaluated in both buffer and biological samples, particularly human urine. The most promising and well-known TB biomarker was lipoarabinomannan (LAM), a bacterial cell wall component. In particular, this biomarker detection was validated with clinical samples from TB patients and healthy donors, showing the ability of our POC platform to discriminate those patients with active TB. Moreover, taking advantage of the photonic sensor design, which allows the simultaneous detection of six different biomarkers, we initiated the proof-of-concept of the POC platform for a TB biomarker panel detection using Dip-Pen Nanolithography for each corresponding bioreceptor deposition. Our results, if validated with larger clinical studies, could have important diagnostic implications taking into account the advantages added by our POC biosensor in comparison with the methods recommended by the World Health Organisation.
Universitat Autònoma de Barcelona. Programa de Doctorat en Biotecnologia

Additive manufacturing in the form of 3D printing is a revolutionary technology that has developed within the last two decades. Its ability to print an object with accurate features down to the micro scale have made its use in medical devices and research feasible. A range of life-saving technologies can now go from the laboratory and into field with the application of 3D-printing. This technology can be applied to medical diagnosis of patients in at-risk populations. Living biosensors are limited by being Genetically Modified Organisms (GMOs) from being employed for medical diagnosis. However, by containing them within a 3D-printed enclosure, these technologies can serve as a vehicle to translate life-saving diagnosis technologies from the laboratory and into the field where the lower cost would allow more people to benefit from inexpensive diagnosis. Also, the GMO biosensors would be contained with a press-fit, ensuring that the living biosensors are unable to escape into the environment without user input. In addition, 3D-printing can also be applied to reduce the cost of lab-based technologies. Cell patterning technology is a target of interest for applying more cost-effective technologies, as elucidation of the variables defining cell patterning and motility may help explain the mechanics of cancer and other diseases. Through the use of a 3D-printed stamp, bacterial cells can be patterning without the use of a clean room, thus lowering the entry-barrier for researchers to explore cell patterning. With the commercialization of 3D-printing an opportunity has arisen to transition life-saving technologies into more cost-effective versions of existing technologies. This would not only allow more research into existing fields, but also to ensure that potentially life-saving technologies reach the people that need them.
Ph. D.

We explore a new laboratory technique in the field of urinalysis promising a combination of speed and selectivity in support of urinary tract infection diagnosis. Laboratory experimentation demonstrates long range surface plasmon polaritons (LRSPP) waveguides as a useful biosensor to selectively detect gram negative bacteria or gram positive bacteria in human urine. The biosensor can detect bacteria at concentration of 105 CFU/ml, the internationally recommended threshold for diagnostic of urinary tract infection (UTI). Using a negative control solution at bacterial concentration 1000x higher than the targeted bacteria in urine with a weak concentration of constituents, the power ratio between the negative control signals to the target bacteria signal is measured to be 5.4. Thus we report a conclusive demonstration of the LRSPP waveguide biosensor selectivity to the gram of bacteria in human urine. In addition, the biosensor may prove useful as an alternative urinalysis test method to determine the urine specific gravity, to estimate proteinuria, and to detect biofilm formation on surfaces.

The explosive development of the telecom industry and in particular wireless and mobile communications in recent years has lead to a rapid development of new component and fabrication technologies to continually satisfy the mutually exclusive requirements for better performance and miniaturization on the one hand and low cost on the other. A fundamental element in radio communications is time and frequency control, which in turn is achieved by high performance electro-acoustic components made on piezoelectric single crystalline substrates. The latter, however, reach their practical limits in terms of performance and cost as the frequency of operation reaches the microwave range. Thus, the thin film electro-acoustic technology, which uses thin piezoelectric films instead, has been recently developed to alleviate these deficiencies. This thesis explores and addresses a number of issues related to thin film synthesis on the one hand as well as component design and fabrication on other. Specifically, the growth of highly c-axis textured AlN thin films has been studied and optimized for achieving high device performance. Perhaps, one of the biggest achievements of the work is the development of a unique process for the deposition of AlN films with a mean c-axis tilt, which is of vital importance for the fabrication of resonators operating in contact with liquids, i.e. biochemical sensors. This opens the way for the development of a whole range of sensors and bio-analytical tools. Further, high frequency Lamb wave resonators have been designed, fabricated and evaluated. Performance enhancement of FBAR devices is also addressed, e.g. spurious mode suppression, temperature compensation, etc. It has been demonstrated, that even without temperature compensation, shear mode resonators operating in a liquid still exhibit an excellent performance in terms of Q (200) and coupling (~1.8%) at 1.2 GHz, resulting in a mass resolution better than 2 ng cm-2 in water, which excels that of today’s quartz sensors.