The reliable quantitative detection of biomarkers and pathogens at picomolar or even lower concentration would be a great help in point-of-care testing but is not readily available today. Integrated optical waveguides, which interact with the biochemical species to be monitored, are promising candidates for the detection of such ultra-low concentrations. The focus of this thesis is on optical waveguides in the shape of micro-ring or micro-racetrack resonators that are manufactured by UV-assisted nanoimprint lithography. This replica manufacturing technology is analyzed using analytical and numerical models in order to identify and quantify the main influence factors that determine the limit of detection of such biosensors. Potential biosensor applications are evaluated and general design rules are derived. The resulting measurements confirm the high potential of the chosen approach with respect to excellent sensitivity, low limit of detection and high dynamic range. With suitable optimization of the sensor layout, a further improvement of the performance by one to two orders of magnitude is possible.:Editor’s Preface Variables and constants Abbreviations 1 Introductions 1.1 Medical laboratory diagnostics 1.2 Biosensor technologies for point-of-care testing 1.3 Integrated optical waveguides and microresonators 1.4 Outline of the thesis 2 Basics 2.1 Guided waves in planar optical waveguides 2.1.1 Planar optical waveguides 2.1.2 Propagation of optical waves 2.1.3 Coupled modes in waveguides 2.2 Planar optical microresonators 2.2.1 Basic layouts and parameters 2.2.2 Manufacturing 2.2.3 Biosensing 2.3 Functionalization and biofunctionalization 3 UV-NIL Polymer Microresonator Biosensor Design 3.1 UV-assisted nanoimprint lithography 3.2 Waveguide cross-sections and refractive indices 3.2.1 Analytical waveguide modeling 3.2.2 Mode diagrams 3.2.3 Conclusions 3.3 Waveguide coupling 3.4 Waveguide losses 3.4.1 Absorption loss 3.4.2 Roughness loss 3.4..3 Substrate loss 3.4.4 Radiation loss due to bending 3.5 Sensitivity of the effective index to analyte binding 3.6 Overall sensitivity and detection limit 3.7 Generic design guidelines 3.8 Parameter selection for UV-NIL polymer waveguides 3.9 Comparison of polymer and silicon-based waveguides 3.9.1 Waveguide geometry 3.9.2 Radiation loss due to bending 3.9.3 Material damping 3.9.4 Surface roughness 3.9.5 Coupling channel widths and coupling coefficients 3.9.6 Conclusions 4 Characterization and Proof of Concept 4.1 Manufacturing-based design limits and chosen designs 4.2 Measurement setup and characterization process 4.3 Optical properties of UV-NIL polymer microresonators 4.4 Proof of concept 4.4.1 Sensitivity to bulk solutions 4.4.2 Reproducibility and drift 4.4.3 Comparison with theory 4.4.4 Comparison with literature 4.4.5 Sensitivity improvement 4.5 Asymmetry of the resonance curves 4.5.1 Cavity lifetime 4.5.2 Thermal influence 4.5.3 Summary 4.6 Conclusions 5 Integration into a biosensor platform 5.1 Chemical functionalization by oxygen plasma 5.2 Preparation of a biosensor characterization assay 5.2.1 Binding of fluorescent nanoparticles onto polymer surfaces 5.3 Microfluidic system 5.3.1 Programmable microfluidic system 5.3.2 System evaluation and improvement 5.4 Conclusions 6 Conclusions Declaration of authorship Acknowledgements Publications and awards / Der zuverlässige quantitative Nachweis von Biomarkern und Krankheitserregern in pikomolarer oder noch niedrigerer Konzentration wäre eine große Hilfe bei Tests am Point-of-Care, ist aber heute nicht ohne weiteres verfügbar. Integrierte optische Wellenleiter, die mit den zu überwachenden biochemischen Spezies interagieren, sind vielversprechende Kandidaten für den Nachweis solcher ultraniedriger Konzentrationen. Der Schwerpunkt dieser Arbeit liegt auf optischen Wellenleitern in Form von Mikro-Ring- oder Mikro-Spur-Resonatoren, die durch UV-unterstützte Nanoimprint-Lithographie hergestellt werden. Diese Replika-Herstellungstechnologie wird mit Hilfe analytischer und numerischer Modelle analysiert, um die wichtigsten Einflussfaktoren zu identifizieren und zu quantifizieren, die die Nachweisgrenze solcher Biosensoren bestimmen. Potenzielle Biosensoranwendungen werden bewertet und allgemeine Designregeln abgeleitet. Die daraus resultierenden Messungen bestätigen das hohe Potenzial des gewählten Ansatzes in Bezug auf ausgezeichnete Empfindlichkeit, niedrige Nachweisgrenze und hohen Dynamikbereich. Bei geeigneter Optimierung des Sensorlayouts ist eine weitere Verbesserung der Leistung um ein bis zwei Größenordnungen möglich.:Editor’s Preface Variables and constants Abbreviations 1 Introductions 1.1 Medical laboratory diagnostics 1.2 Biosensor technologies for point-of-care testing 1.3 Integrated optical waveguides and microresonators 1.4 Outline of the thesis 2 Basics 2.1 Guided waves in planar optical waveguides 2.1.1 Planar optical waveguides 2.1.2 Propagation of optical waves 2.1.3 Coupled modes in waveguides 2.2 Planar optical microresonators 2.2.1 Basic layouts and parameters 2.2.2 Manufacturing 2.2.3 Biosensing 2.3 Functionalization and biofunctionalization 3 UV-NIL Polymer Microresonator Biosensor Design 3.1 UV-assisted nanoimprint lithography 3.2 Waveguide cross-sections and refractive indices 3.2.1 Analytical waveguide modeling 3.2.2 Mode diagrams 3.2.3 Conclusions 3.3 Waveguide coupling 3.4 Waveguide losses 3.4.1 Absorption loss 3.4.2 Roughness loss 3.4..3 Substrate loss 3.4.4 Radiation loss due to bending 3.5 Sensitivity of the effective index to analyte binding 3.6 Overall sensitivity and detection limit 3.7 Generic design guidelines 3.8 Parameter selection for UV-NIL polymer waveguides 3.9 Comparison of polymer and silicon-based waveguides 3.9.1 Waveguide geometry 3.9.2 Radiation loss due to bending 3.9.3 Material damping 3.9.4 Surface roughness 3.9.5 Coupling channel widths and coupling coefficients 3.9.6 Conclusions 4 Characterization and Proof of Concept 4.1 Manufacturing-based design limits and chosen designs 4.2 Measurement setup and characterization process 4.3 Optical properties of UV-NIL polymer microresonators 4.4 Proof of concept 4.4.1 Sensitivity to bulk solutions 4.4.2 Reproducibility and drift 4.4.3 Comparison with theory 4.4.4 Comparison with literature 4.4.5 Sensitivity improvement 4.5 Asymmetry of the resonance curves 4.5.1 Cavity lifetime 4.5.2 Thermal influence 4.5.3 Summary 4.6 Conclusions 5 Integration into a biosensor platform 5.1 Chemical functionalization by oxygen plasma 5.2 Preparation of a biosensor characterization assay 5.2.1 Binding of fluorescent nanoparticles onto polymer surfaces 5.3 Microfluidic system 5.3.1 Programmable microfluidic system 5.3.2 System evaluation and improvement 5.4 Conclusions 6 Conclusions Declaration of authorship Acknowledgements Publications and awards

Molding is a simple manufacturing process whereby fluid fills a master tool and then solidifies in the shape of the tool cavity. The precise nature of material flow during molding has long allowed fabrication of plastic components with sizes 1 mm 1 m. Polymer molding with precise critical dimension control could enable scalable, inexpensive production of micro- and nanostructures for functional or lithographic use. This dissertation reports experiments and simulations on molding of polymer micro- and nanostructures at length scales 1 nm 1 mm. The research investigates two main areas: 1) mass transport during micromolding and 2) polymer mechanical properties during nanomolding at length scales 100 nm. Measurements and simulations of molding features of size 100 nm 1 mm show local mold geometry modulates location and rate of polymer shear and determines fill time. Dimensionless ratios of mold geometry, polymer thickness, and bulk material and process properties can predict flow by viscous or capillary forces, shape of polymer deformation, and mold fill time. Measurements and simulations of molding at length scales 100 nm show the importance of nanoscale physical processes distinct from bulk during mechanical processing. Continuum simulations of atomic force microscope nanoindentation accurately model sub-continuum polymer mechanical response but highlight the need for nanoscale material property measurements to accurately model deformation shape. The development of temperature-controlled nanoindentation enables characterization of nanoscale material properties. Nanoscale uniaxial compression and squeeze flow measurements of glassy and viscoelastic polymer show film thickness determines polymer entanglement with cooperative polymer motions distinct from those observed in bulk. This research allows predictive design of molding processes and highlights the importance of nanoscale mechanical properties that could aid understanding of polymer physics.

Thermal nanoimprint lithography (T-NIL) is a cheap and fast technique to produce nanopatterns in polymeric materials. It creates these patterns by pressing a stamp down into a polymer film that has been heated above its glass transition temperature. These nanopatterned polymer films can be used in a wide variety of scientific fields, not the least the organic semiconductor industry. There the nanopatterned films have, among else, been used to improve the efficiency of organic light-emitting diodes (OLEDs). The light-emitting electrochemical cell (LEC), which is similar in structure to an OLED, also uses polymer films in their device structure but the light emitting layer also contains an electrolyte. However, it has not been shown if nanopatterns can improve LECs as well or if it is even possible to make an imprint in their polymer films that are mixed with an electrolyte. This thesis shows that T-NIL can be used to imprint nanopatterns in films made of poly(ethylene oxide) and the conjugated polymer Super Yellow. The best nanopatterns were produced by setting the imprint parameters to  85 °C, 10 bar, 1800 s for poly(ethylene oxide) and 115 °C, 20 bar, 1800 s for Super Yellow. Imprints were also performed on polystyrene but no nanopatterns could be produced. This was most likely because the stamp could not handle the high temperature that is required to make a nanopattern in polystyrene. The best imprint parameters of Super Yellow were then used to produce a pattern in a film made of Super Yellow mixed with the salt tetrahexylammonium tetrafluoroborate (THABF4) in order to be able to produce one imprinted and one reference LEC. The imprinted LEC had a luminosity of 139 cd/m2, an improvement of 20% compared to the reference’s 115 cd/m2 when operated under identical conditions.  The forward direction and the angular dependent electroluminescence spectrum of the imprinted LEC clearly showed an effect not observed in the reference. These findings show that the polymer films used in a LEC can be imprinted with a nanopattern by using T-NIL. The imprinted films can be used to create functional LECs that show different behavior and a higher luminosity compared to a non-imprinted reference. If these results can be repeated it might be the starting point of a brighter future.

To increase the survival rate from infectious- and noncommunicable diseases, reliable diagnostic during the preliminary stages of a disease onset is of vital importance. This is not trivial to achieve, a highly sensitive and selective detection system is needed for measuring the low concentrations of biomarkers available. One possible route to achieve this is through biosensing based on plasmonic nanostructures, which during the last decade have demonstrated impressive diagnostic capabilities. These nanoplasmonic surfaces have the ability to significantly enhance fluorescence- and Raman signals through localized hotspots, where a stronger then normal electric field is present. By further utilizing a periodic sub-wavelength nanohole array the extraordinary optical transmission phenomena is supported, which open up new ways for miniaturization. In this study a nanoplasmonic chip (NPC) composed of a nanohole array —with lateral size on the order of hundreds of nanometer— covered in a thin layer of gold is created. The nanohole array is fabricated using soft nanoimprint lithography on two resists, hydroxypropyl cellulose (HPC) and polymethyl methacrylate (PMMA). An in depth analysis of the effect of thickness is done, where the transmittance and Raman scattering (using rhodamine 6G) are measured for varying gold layers from 5 to 21 nm. The thickness was proved to be of great importance for optimizing the Raman enhancement, where a maximum was found at 13 nm. The nanohole array were also in general found beneficial for additionally enhancing the Raman signal. A transmittance minima and maxima were found in the region 200-1000 nm for the NPCs, where the minima redshifted as the thickness increased. The extraordinary transmission phenomena was however not observed at these thin gold layers. Oxygen plasma treatment further proved an effective treatment method to reduce the hydrophobic properties of the NPCs. Care needs be taken when using thin layers of gold with a PMMA base, as the PMMA structure could get severely damaged by the plasma. HPC also proved inadequate for this projects purpose, as water-based fluids easily damaged the surface despite a deposited gold layer on top.