This thesis describes work carried out on the research, development and implementation of new processes for the fabrication of surface plasmon waveguide biosensors. Fabrication of surface plasmon resonance (SPR) based waveguides embedded in a thick CYTOP cladding with the incorporation of fluidic channels was achieved with improved quality and operability compared to previous attempts. The fabrication flow was modified in key areas including lithography for feature definition, gold evaporation and the upper cladding deposition procedure. The combined result yielded devices with sharper resolution of waveguides, gold surfaces with minimal aberrations, reduced surface roughness and minimization of waveguide deformation due to reduction of solvent diffusion into the lower cladding. The fabricated waveguides consisted of a thin, 35 nm, patterned gold film, embedded in a thick, 18 µm, CYTOP fluoroploymer cladding. The gold devices were exposed by O2 plasma etching through the upper cladding to form fluidic channels for the facilitation of flow of an index matched sensing medium. Optical and physical characterization of devices revealed structures of significantly improved quality over previous attempts, rendering the platform competitive for biosensing applications.

This thesis describes work carried out on the research, development and implementation of new processes for the fabrication of surface plasmon waveguide biosensors. Fabrication of surface plasmon resonance (SPR) based waveguides embedded in a thick CYTOP cladding with the incorporation of fluidic channels was achieved with improved quality and operability compared to previous attempts. The fabrication flow was modified in key areas including lithography for feature definition, gold evaporation and the upper cladding deposition procedure. The combined result yielded devices with sharper resolution of waveguides, gold surfaces with minimal aberrations, reduced surface roughness and minimization of waveguide deformation due to reduction of solvent diffusion into the lower cladding. The fabricated waveguides consisted of a thin, 35 nm, patterned gold film, embedded in a thick, 18 µm, CYTOP fluoroploymer cladding. The gold devices were exposed by O2 plasma etching through the upper cladding to form fluidic channels for the facilitation of flow of an index matched sensing medium. Optical and physical characterization of devices revealed structures of significantly improved quality over previous attempts, rendering the platform competitive for biosensing applications.

This thesis describes work carried out on the research, development and implementation of new processes for the fabrication of surface plasmon waveguide biosensors. Fabrication of surface plasmon resonance (SPR) based waveguides embedded in a thick CYTOP cladding with the incorporation of fluidic channels was achieved with improved quality and operability compared to previous attempts. The fabrication flow was modified in key areas including lithography for feature definition, gold evaporation and the upper cladding deposition procedure. The combined result yielded devices with sharper resolution of waveguides, gold surfaces with minimal aberrations, reduced surface roughness and minimization of waveguide deformation due to reduction of solvent diffusion into the lower cladding. The fabricated waveguides consisted of a thin, 35 nm, patterned gold film, embedded in a thick, 18 µm, CYTOP fluoroploymer cladding. The gold devices were exposed by O2 plasma etching through the upper cladding to form fluidic channels for the facilitation of flow of an index matched sensing medium. Optical and physical characterization of devices revealed structures of significantly improved quality over previous attempts, rendering the platform competitive for biosensing applications.

Low temperature-processed, porous sol-gel glasses represent a new class of materials for the immobilisation of biomolecules. If used to entrap biological recognition elements, these transparent and chemically inert glasses offer a new approach in the development of optical biosensors.

<p> The goal of this research project was the development of a protocol for preparation of optically clear organic/inorganic hybrid materials that was amenable to entrapment of lipophilic biomolecules. The protocol involved the acid-catalyzed hydrolysis of mixtures of tetraethylorthosilicate (TEOS) with organosilane precursors, including methyltriethoxysilane (MTES), dimethyldimethoxysilane (DMDMS) and propyltrimethoxysilane (PTMS) in the presence and absence of the polymer additives poly(ethylene glycol) or poly(vinyl alcohol).</p> <p> The effect of organosilane precursors and polymer additives on the optical clarity, hardness and hydration stability of the resulting materials was characterized. It was determined that there was a limit to the amount of organosilane that could be added before the materials exhibited unacceptable characteristics. These limits were 20.0% (v/v) for MTES, 10.0% (v/v) for PTMS, and 5.0% (v/v) for DMDMS. Addition of PEG to these materials at levels up to 10.0% (w/v) resulted in good material characteristics. However, addition of PVA produced opaque materials with poor material properties. The internal environment of the materials was also probed using the environmentally sensitive fluorescent probes 7-azaindole (7AI) and prodan. These studies showed that the method of hydrolysis of the silane precursors and the aging conditions had a dramatic effect on the resulting material.</p> <p> The hybrid materials were used to entrap human serum albumin (HSA) and lipase to determine the effect of organic content on the biological function of these biomolecules. Both biomolecules retained a portion of their native function when entrapped in sol-gel-derived materials, and it was found that both proteins showed enhanced function in the presence of MTES. In the case of lipase, it was also determined that addition of PEG 600 at 10.0% (w/v in the gelation buffer) provided a dramatic increase in activity compared to materials without this additive, likely owing to a direct effect of the PEG on the stability of the entrapped protein.</p> <p> Following studies using bulk glasses, a protocol was developed for the preparation of optically clear sol-gel-derived thin films that was amenable to entrapment of biomolecules. The optimal method involved dipcasting of co-hydrolyzed materials containing 1.0 to 3.0% PEG. By careful control of the viscosity of the casting solution and the rate of film deposition, it was possible to form very stable thin films with excellent physical characteristics. These films were used to entrap the pH-sensitive, ratiometric fluorescent probe dextran-SNARF-1, resulting in a prototype of a fluorimetric pH sensor. Co-entrapment of the probe and lipase into sol-gel-derived thin films resulted in a rapid, reagentless biosensor prototype that could monitor changes in pH due to the enzyme-catalyzed hydrolysis of triglycerides. These results demonstrate that species entrapped in sol-gel derived thin films are suitable for biosensor development.</p> / Thesis / Master of Science (MSc)

Um Luminescent Solar Concentrators (LSC) é basicamente uma base plástica transparente ou vidro contendo centros luminescentes.Enquanto o recente avanço dos conversores de comprimento de onda tenha aberto novas possibilidades para o desenvolvimento de células solares mais eficientes, estes também abriram novas frentes de pesquisa.Uma destas frentes envolve os problemas encontrados com o uso de novos materiais. Como por exemplo, transferência de energia em polímeros. Surgem propriedades interessantes a respeito dos processos luminescentes ao longo destes sistemas planares.Por estes motivos esses sistemas podem ser aplicados como dispositivos optoeletrônicos, sensores e também em conversores de comprimento de onda. Este estudo descreve a fabricação de guias de onda planares multipoliméricos baseados em uma matrix acrílica (PMMA) dopada com polímeros emissores de luz. A função desta blenda polimérica é absorver um largo espectro de luz e re-emitir ao longo do guia de onda. Os dispositivos foram estudados em termos de suas características de absorção, emissão e excitação.Os polímeros emissores utilizados neste trabalho foram: MEH-PPV, Super Yellow, ADS-108GE, ADS-329BE, e LAPS-16. Estes materiais foram dissolvidos em tolueno e depositados pela técnica casting sobre substratos de vidro contendo filmes metálicos de alumínio.Usando esta configuração, a luz de excitação incidente é acoplada ao guia de onda por absorção e re-emissão através dos polímeros luminescentes. O estudo dos LSCs é realizado por medidas das emissões laterais e normais dos guias. Estes guias apresentam um espectro de emissão com características típicas de uma cavidade do tipo Fabri-Perot, com linhas extremamente estreitas (3 nm) e altamente polarizadas na direção paralela (modo TE) e perpendicular (TM) ao plano do guia de onda.A emissão destes guias é fortemente dependente de sua geometria e do índice de refração efetivo. Os mesmos filmes poliméricos, porém mais espessos (30 m), foram utilizados como conversores de comprimento de onda visando aplicação em conversores solares luminescentes (Luminescence Solar Converters, ou LSCs). O uso de baixas concentrações das moléculas utilizadas foi necessário para evitar possíveis formações de agregados quando altas concentrações de PMMA são utilizadas na preparação dos filmes. A metalização de uma das faces planares possibilitou o aumento da eficiência de conversão dos comprimentos de onda nos LSCs. A luminescência total dos polímeros é completamente convertida em luz de alto comprimento de onda na emissão lateral.Este processo não depende do comprimento de onda de excitação. A metalização de uma das faces planares possibilitou o aumento da eficiência de conversão dos LSCs. Neste sistema, a luz absorvida é convertida em luz de alto comprimento de onda e alta pureza espectral através de processos de reabsorção, relaxação interna e re-emissão que ocorrem ao longo do plano do LSC. A eficiência de conversão e as perdas em função da concentração polimérica na matriz foram estudadas para os LSCs.O escape dos fótons nas interfaces para ângulos menores que o ângulo crítico (c=arcsen(1/n)) e processos de transferência de energia em LSCs com alta concentração polimérica devem ser otimizados para sua aplicação como dispositivos. / Luminescent Solar Concentrators (LSC) are basically composed of a transparent plastic or glass substrate containing luminescent centers.While the recent advance in wavelength converters has opened up many new possibilities for development of more efficient photovoltaic cells, they have also raised new issues. A number of these issues involve problems of dealing with new materials and the understanding of physical process like energy transfer in polymers. Interesting features arise from the luminescent process along these planar systems. Therefore this system can be applied as optoelectronics devices, sensors and also in wavelength converters. This study describes the fabrication of planar multi-polymeric optical waveguides based on acrylic matrix (PMMA) doped with a light emitting polymers. The function of thispolymeric blendis to absorb a broad spectrum of light and re-emit it along the waveguide. The devices were studied in terms of its absorption, emission and excitation characteristics.The emitting polymers used in this research are: poly[2-methoxy-5-(2-ethyl-hexyloxy)-1,4-phenylenevinylene] (MEH-PPV), Super Yellow, Poly[(9,9-dioctyl-2,7-divinylenefluorenylene)-alt-co-{2-methoxy-5-(2-ethyl-hexyloxy)-1,4-phenylene}] called ADS108GE, Poly(9,9-dioctylfluorenyl-2,7-diyl) called ADS239BE, and poli-(9,9-n-dihexil-2,7-fluorenodilvinilene-alt-1,4-fenilenovinileno) or Laps16. Films of these materials dissolved in toluene were deposited by casting the polymethacrylate solution on top of a glass substrate containing a reflective aluminum layer. Using this configuration, the incident excitation light is coupled to the wave guide by its absorption and then re-emitted by the luminescent polymers. The LSCs characterization was carried out by measuring the lateral and the normal emissions of the guide. These waveguides show a light emission spectrum with characteristics similar to the Fabri-Perot cavity, where very narrow peaks (3 nm) and highly polarized emission in both TE and TM modes were observed. In addition, the emission is strongly dependent on its geometry and the effective refraction index. In other hand, thicker polymeric guides (30 m) were used as luminescence solar converters (LSCs). The optimal concentration of conjugated polymers solutions has to be very low in order to avoid the formation of aggregates since high PMMA concentrations have to be used in the LSC preparation.The total polymeric luminescence is fully converted to light of high wavelength for the case of lateral emission. This process does not depend on the excitation wavelength. The conversion efficiency was increased by evaporating metals on one planar face of the LSC. In this structure, light is absorbed and then converted to a higher wavelength with high spectral pureness through re-absorption, relaxation and re-emission processes occurring along the LSC plane. The conversion efficiency and the losses along the converter were studied as a function of the polymeric concentration, in order to optimize these structures. A better understanding of the process of energy transfer and photon leakage through the interfaces for angles smaller than the critical angle (c=arcsen(1/n)) is necessary for using LSCs as applied devices.

Um Luminescent Solar Concentrators (LSC) é basicamente uma base plástica transparente ou vidro contendo centros luminescentes.Enquanto o recente avanço dos conversores de comprimento de onda tenha aberto novas possibilidades para o desenvolvimento de células solares mais eficientes, estes também abriram novas frentes de pesquisa.Uma destas frentes envolve os problemas encontrados com o uso de novos materiais. Como por exemplo, transferência de energia em polímeros. Surgem propriedades interessantes a respeito dos processos luminescentes ao longo destes sistemas planares.Por estes motivos esses sistemas podem ser aplicados como dispositivos optoeletrônicos, sensores e também em conversores de comprimento de onda. Este estudo descreve a fabricação de guias de onda planares multipoliméricos baseados em uma matrix acrílica (PMMA) dopada com polímeros emissores de luz. A função desta blenda polimérica é absorver um largo espectro de luz e re-emitir ao longo do guia de onda. Os dispositivos foram estudados em termos de suas características de absorção, emissão e excitação.Os polímeros emissores utilizados neste trabalho foram: MEH-PPV, Super Yellow, ADS-108GE, ADS-329BE, e LAPS-16. Estes materiais foram dissolvidos em tolueno e depositados pela técnica casting sobre substratos de vidro contendo filmes metálicos de alumínio.Usando esta configuração, a luz de excitação incidente é acoplada ao guia de onda por absorção e re-emissão através dos polímeros luminescentes. O estudo dos LSCs é realizado por medidas das emissões laterais e normais dos guias. Estes guias apresentam um espectro de emissão com características típicas de uma cavidade do tipo Fabri-Perot, com linhas extremamente estreitas (3 nm) e altamente polarizadas na direção paralela (modo TE) e perpendicular (TM) ao plano do guia de onda.A emissão destes guias é fortemente dependente de sua geometria e do índice de refração efetivo. Os mesmos filmes poliméricos, porém mais espessos (30 m), foram utilizados como conversores de comprimento de onda visando aplicação em conversores solares luminescentes (Luminescence Solar Converters, ou LSCs). O uso de baixas concentrações das moléculas utilizadas foi necessário para evitar possíveis formações de agregados quando altas concentrações de PMMA são utilizadas na preparação dos filmes. A metalização de uma das faces planares possibilitou o aumento da eficiência de conversão dos comprimentos de onda nos LSCs. A luminescência total dos polímeros é completamente convertida em luz de alto comprimento de onda na emissão lateral.Este processo não depende do comprimento de onda de excitação. A metalização de uma das faces planares possibilitou o aumento da eficiência de conversão dos LSCs. Neste sistema, a luz absorvida é convertida em luz de alto comprimento de onda e alta pureza espectral através de processos de reabsorção, relaxação interna e re-emissão que ocorrem ao longo do plano do LSC. A eficiência de conversão e as perdas em função da concentração polimérica na matriz foram estudadas para os LSCs.O escape dos fótons nas interfaces para ângulos menores que o ângulo crítico (c=arcsen(1/n)) e processos de transferência de energia em LSCs com alta concentração polimérica devem ser otimizados para sua aplicação como dispositivos. / Luminescent Solar Concentrators (LSC) are basically composed of a transparent plastic or glass substrate containing luminescent centers.While the recent advance in wavelength converters has opened up many new possibilities for development of more efficient photovoltaic cells, they have also raised new issues. A number of these issues involve problems of dealing with new materials and the understanding of physical process like energy transfer in polymers. Interesting features arise from the luminescent process along these planar systems. Therefore this system can be applied as optoelectronics devices, sensors and also in wavelength converters. This study describes the fabrication of planar multi-polymeric optical waveguides based on acrylic matrix (PMMA) doped with a light emitting polymers. The function of thispolymeric blendis to absorb a broad spectrum of light and re-emit it along the waveguide. The devices were studied in terms of its absorption, emission and excitation characteristics.The emitting polymers used in this research are: poly[2-methoxy-5-(2-ethyl-hexyloxy)-1,4-phenylenevinylene] (MEH-PPV), Super Yellow, Poly[(9,9-dioctyl-2,7-divinylenefluorenylene)-alt-co-{2-methoxy-5-(2-ethyl-hexyloxy)-1,4-phenylene}] called ADS108GE, Poly(9,9-dioctylfluorenyl-2,7-diyl) called ADS239BE, and poli-(9,9-n-dihexil-2,7-fluorenodilvinilene-alt-1,4-fenilenovinileno) or Laps16. Films of these materials dissolved in toluene were deposited by casting the polymethacrylate solution on top of a glass substrate containing a reflective aluminum layer. Using this configuration, the incident excitation light is coupled to the wave guide by its absorption and then re-emitted by the luminescent polymers. The LSCs characterization was carried out by measuring the lateral and the normal emissions of the guide. These waveguides show a light emission spectrum with characteristics similar to the Fabri-Perot cavity, where very narrow peaks (3 nm) and highly polarized emission in both TE and TM modes were observed. In addition, the emission is strongly dependent on its geometry and the effective refraction index. In other hand, thicker polymeric guides (30 m) were used as luminescence solar converters (LSCs). The optimal concentration of conjugated polymers solutions has to be very low in order to avoid the formation of aggregates since high PMMA concentrations have to be used in the LSC preparation.The total polymeric luminescence is fully converted to light of high wavelength for the case of lateral emission. This process does not depend on the excitation wavelength. The conversion efficiency was increased by evaporating metals on one planar face of the LSC. In this structure, light is absorbed and then converted to a higher wavelength with high spectral pureness through re-absorption, relaxation and re-emission processes occurring along the LSC plane. The conversion efficiency and the losses along the converter were studied as a function of the polymeric concentration, in order to optimize these structures. A better understanding of the process of energy transfer and photon leakage through the interfaces for angles smaller than the critical angle (c=arcsen(1/n)) is necessary for using LSCs as applied devices.

Title: Multifunctional biomolecular assemblies for parallelized analysis of biomolecular interactions Author: Markéta Bocková Department / Institute: Institute of Physics, Charles University Supervisor of the doctoral thesis: Prof. Jiří Homola, Ph.D., DSc., Institute of Photonics and Electronics, The Czech Academy of Sciences Abstract: Surface plasmon resonance (SPR) biosensors represent the most advanced optical method for the direct, real-time monitoring of biomolecular interactions without the need for labelling. This doctoral thesis aims to advance the SPR biosensor method and to expand its utility in the investigation of biomolecular interactions. This encompasses activities on two major fronts of SPR biosensor research - immobilization methods and biosensing methodologies. Methods for the immobilization of biomolecules were researched with the aim of enabling the immobilization of a broad range of biomolecules on the SPR biosensor surface in a spatially controlled manner. The development of novel biosensing methodologies was pursued in order to address the current limitations of SPR biosensors associated with non-specific adsorption and limited analyte transport, and thus to improve the accuracy and robustness of SPR biosensor measurements. Finally, advances in the development of immobilization...

In this thesis by articles, I propose and demonstrate the full design, fabrication and characterization of optical biosensors based on (Bloch) Long Range Surface Plasmon Polaritons (LRSPPs). Gold waveguides embedded in CYTOP with an etched microfluidic channel supporting LRSPPs and gold waveguides on a one-dimensional photonic crystal (1DPC) supporting Bloch LRSPPs are exploited for biosensing applications. Straight gold waveguides embedded in CYTOP supporting LRSPPs as a biosensor, are initially used to measure the kinetics constants of protein-protein interactions. The kinetics constants are extracted from binding curves using the integrated rate equation. Linear and non-linear least squares analysis are employed to obtain the kinetics constants and the results are compared. The device is also used to demonstrate enhanced assay formats (sandwich and inhibition assays) and protein concentrations as low as 10 pg/ml in solution are detected with a signal-to-noise ratio of 20 using this new optical biosensor technology. CYTOP which has a refractive index close to water is the fluoropolymer of choice in current state of the art waveguide biosensors. CYTOP has a low glass transition temperature which introduces limitations in fabrication processes. A truncated 1D photonic crystal can replace a low-index polymer cladding such as CYTOP, to support Bloch LRSPPs within the bandgap of the 1DPC over a limited ranges of wavenumber and wavelength. Motivated by quality issues with end facets, we seek to use grating couplers in a broadside coupling scheme where a laser beam emerging from an optical fiber excites Bloch LRSPPs on a Au stripe on a truncated 1D photonic crystal. Adiabatic and non-adiabatic flared stripes accommodating wide gratings size-matched to an incident Gaussian beam are designed and compared to maximise the coupling efficiency to LRSPPs. The gratings are optimized, initially, through 2D modelling using the vectorial finite element method (FEM). Different 3D grating designs were then investigated via 3D modelling using the vectorial finite difference time domain (FDTD) method. Given their compatibility with planar technologies, gratings and waveguides can be integrated into arrays of biosensors enabling multi-channel biosensing. A multi-channel platform can provide, e.g., additional measurements to improve the reliability in a disease detection problem. Thus, a novel optical biosensor based on Bloch LRSPPs on waveguide arrays integrated with electrochemical biosensors is presented. The structures were fabricated on truncated 1D photonic crystals comprised of 15 period stack of alternating layers of SiO2/Ta2O5. The optical biosensors consist of Au stripes supporting Bloch LRSPPs and integrate grating couplers as input/output means. The Au stripes also operate as a working electrode in conjunction with a neighboring Pt counter electrode to form an electrochemical sensor. The structures were fabricated using bilayer lift-off photolithography and the gratings were fabricated using overlaid e-beam lithography. The planar waveguides are integrated into arrays capable of multichannel biosensing. The wafer is covered with CYTOP as the upper cladding with etched microfluidic channels, and wafer-bonded to a borofloat silica wafer to seal the fluidic channels and enable side fluidic interfaces. The proposed device is capable in principle of simultaneous optical and electrochemical sensing and could be used to address disease detection problems using a multimodal strategy.

Optical biosensors are increasingly being considered for lab-on-a-chip applications due to their benefits such as small size, biocompatibility, passive behaviour and lack of the need for fluorescent labels. The light guiding mechanisms used by many of them result in poor overlap of the optical field with the target molecules, reducing the maximum sensitivity achievable. This thesis presents a new platform for optical biosensors, namely slotted photonic crystals, which engender higher sensitivities due to their ability to confine, spatially and temporally, the peak of optical mode within the analyte itself. Loss measurements showed values comparable to standard photonic crystals, confirming their ability to be used in real devices. A novel resonant coupler was designed, simulated, and experimentally tested, and was found to perform better than other solutions within the literature. Combining with cavities, microfluidics and biological functionalization allowed proof-of-principle demonstrations of protein binding to be carried out. High sensitivities were observed in smaller structures than most competing devices in the literature. Initial tests with cellular material for real applications was also performed, and shown to be of promise. In addition, groundwork to make an integrated device that includes the spectrometer function was also carried out showing that slotted photonic crystals themselves can be used for on-chip wavelength specific filtering and spectroscopy, whilst gas-free microvalves for automation were also developed. This body of work presents slotted photonic crystals as a realistic platform for complete on-chip biosensing; addressing key design, performance and application issues, whilst also opening up exciting new ideas for future study.