Livet tas för givet av de flesta. Det finns däremot många som ägnar stora delar av sitt liv för att försöka lösa dess mysterier. En del av lösningen ligger i att förstå hur alla molekyler är sammanlänkade i det gigantiska nätverk som definierar den levande organismen. Under det senaste seklet har en hel del forskning utförts för att kartlägga dessa nätverk. Resultatet av dessa mödor kan vi se i de läkemedel som vi har idag och som har utvecklats för att bota eller åtminstone lindra olika sjukdomar och tillstånd. Dessvärre finns det fortfarande många sjukdomar som är obotliga (t.ex. cancer) och mycket arbete krävs för att förstå dem till fullo och kunna designa framgångsrika behandlingar. Arbetet i denna avhandling beskriver en analytisk plattform som kan användas för att effektivisera kartläggningsprocessen; protein-mikroarrayer. Mikroarrayer är ytor som har mikrometerstora (tusendels millimeter) strukturer i ett regelbundet mönster med möjligheten att studera många interaktioner mellan biologiska molekyler samtidigt. Detta medför snabbare och fler analyser - till en lägre kostnad. Protein-mikroarrayer har funnits i ungefär ett decennium och har följt i fotspåren av de framgångsrika DNA-mikroarrayerna. Man bedömer att protein-mikroarrayerna har en minst lika stor potential som DNA mikroarrayerna då det egentligen är mer relevant att studera proteiner, som är de funktionsreglerande molekylerna i en organism. Vi har i detta arbete tillverkat modellytor för stabil inbindning av proteiner, som lämnar dem intakta, funktionella och korrekt orienterade i ett mikroarray format. Därmed har vi adresserat ett stort problem med protein mikroarrays, nämligen att proteiner är känsliga molekyler och har i många fall svårt att överleva tillverkningsprocessen av mikroarrayerna. Vi har även studerat en metod att tillverka mikroarrayer av proteiner bundna till strukturer, som modellerats att efterlikna cellytor. Detta är särkilt viktigt eftersom många (hälften) av dagens (och säkerligen framtidens) läkemedel är riktade mot att påverka denna typ av proteiner och att studera dessa i sin naturliga miljö är därför väldigt relevant. I ett annat projekt har vi använt protein mikroarrayer för att detektera fyra vanliga droger (heroin, amfetamin, ecstasy och kokain). Detektionen baseras på användandet av antikroppar som lossnar från platser på ytan när de kommer i kontakt med ett narkotikum. Detta koncept kan enkelt utvecklas till att detektera mer än bara fyra droger. Vi har även lyckats att parallellt mäta förekomsten av en annan typ av förening på mikroarray ytan, nämligen det explosiva ämnet trinitrotoluen (TNT). Detta visar på en mångsidig plattform för detektionen av i princip vilken typ av farlig eller olaglig substans som helst - och på en yta! Vi föreställer oss därför att möjliga tillämpningsområden finns inom brottsbekämpning, i kampen mot terrorism och mot narkotikamissbruk etc. Mikroarrayerna har i denna avhandling utforskats med optiska metoder som tillåter studie av omärkta proteiner, vilket resulterar i så naturliga molekyler som möjligt. / Life is a thing taken for granted by most. However, it is the life-long quest of many to unravel the mysteries of it. Understanding and characterizing the incomprehensively complex molecular interaction networks within a biological organism, which defines that organism, is a vital prerequisite to understand life itself. Already, there has been a lot of research conducted and a large knowledge has been obtained about these pathways over, especially, the last century. We have seen the fruits of these labors in e.g. the development of medicines which have been able to cure or at least arrest many diseases and conditions. However, many diseases are still incurable (e.g. cancer) and a lot more work is still needed for understanding them fully and designing successful treatments. This work describes a generic analytical tool platform for aiding in more efficient (bio)molecular interaction mapping analyses; protein microarray chips. Microarray chips are surfaces with micrometer sized features with the possibility of studying the interactions of many (thousands to tens of thousands) (bio)molecules in parallel. This allows for a higher throughput of analyses to be performed at a reduced time and cost. Protein microarrays have been around for approximately a decade, following in the footsteps of the, so far, more successfully used DNA microarrays (developed in the 1990s). Microarrays of proteins are more difficult to produce because of the more complex nature of proteins as compared to DNA. In our work we have constructed model surfaces which allow for the stable, highly oriented, and functional immobilization of proteins in an array format. Our capture molecules are based on multivalent units of the chelator nitrilotriacetic acid (NTA), which is able to bind histidine-tagged proteins. Furthermore, we have explored an approach for studying lipid membrane bound systems, e.g. receptor-ligand interactions, in a parallelized, microarray format. The approach relies on the addressable, DNA-mediated adsorption of tagged lipid vesicles. In an analogous work we have used the protein microarray concept for the detection of four common narcotics (heroin, amphetamine, ecstasy, and cocaine). The detection is based on the displacement of loosely bound antibodies from surface array positions upon injection of a specific target analyte, i.e. a narcotic substance. The proof-of-concept chip can easily be expanded to monitor many more narcotic substances. In addition, we have also been able to simultaneously detect the explosive trinitrotoluene (TNT) along with the narcotics, showing that the chip is a versatile platform for the detection of virtually any type of harmful or illegal compound. This type of biosensor system is potentially envisaged to be used in the fight against crime, terrorism, drug abuse etc. Infrared reflection absorption spectroscopy together with ellipsometry has been used to characterize molecular layers used in the fabrication processes of the microarray features. Imaging surface plasmon resonance operating in the ellipsometric mode is subsequently used for functional evaluation of the microarrays using a well-defined receptor-ligand model system. This approach allows simultaneous and continuous monitoring of binding events taking place in multiple regions of interest on the microarray chip. A common characteristic of all the instrumentation used is that there is no requirement for labeling of the biomolecules to be detected, e.g. with fluorescent or radioactive probes. This feature allows for a flexible assay design and the use of more native proteins, without any time-consuming pretreatments.

The main objective of this thesis is to study the polarization effects of the beetle Cetonia aurata using Mueller-matrix ellipsometry. The outer shell of the beetle consists of complex microstructures which control the polarization of the reflected light. It has metallic appearance which originates from helicoidal structures. When these microstructures are exposed to polarized or unpolarized light, only left-handed circularly polarized light is reflected. Moreover, the exo-skeleton of the beetle absorbs right-handed polarized light. Multichannel Mueller-matrix ellipsometer or dual rotating compensator ellipsometer, called RC2, from J.A.Woollam is used to measure the polarization caused by different parts of beetle’s body. The 16 Mueller matrix elements are measured in the spectral range 400-800 nm at multiple angles of incidencein the range 400-700. An Optical model is developed to help us understand the nature and type of microstructure which only reflects the green colour circularly polarized light. With the help of multiparametric modeling, we were able to find optical properties and structural parameters. The parameters are: the number of layers, the numbers of sub-layers, their thicknesses, and the orientation with respect to optical axes. This optical model describes the nanostructures which provide the reflection properties similar to the nanostructure found in the beetle Cetonia aurata. The model is also useful for analysis of the optical response data of different materials with multilayer structures.

This master thesis aimed to create and characterize multilayer coatings upon mesoporous silica particles (MSP). The properties of the coating aimed for, was to have a triggerable controlled release, where a targeted enzyme within the intestine, alpha-amylase, is supposed to degrade the coating. The coating was created from a bilayer consisting of DOTAP and DOPC in a 1:3 molar ratio, which serves as a protective coating. The second layer interacting with the surroundings consisted of a starch component, amylopectin, which is degraded by alpha-amylase. The study of the coating was performed with ellipsometry, where the adsorption of the different layers of the coating on a planar silica surface and the enzyme-triggered degradation was recorded. The adsorbed amount of DOTAP/DOPC was 4,22 ± 0,11 mg/m2 and amylopectin 1,82 ± 0,94. The effects of different pH where performed, simulating the coated particle going through the gastro-intestinal system. Two enzymes alpha-amylase and phospholipase A2 (PLA2) where used for degradation of the coating. The knowledge from ellipsometry was applied to coating mesoporous silica particles and it was confirmed that the two layers had formed with zeta- potential measurement.

The polarization behaviour for six species of Scarab beetles from the Chrysina genus is investigated with Mueller Matrix Spectroscopic Ellipsometer (MMSE). The m41 element of the matrix, which is related to the circular polarization behaviour, is analysed. The ellipticity, degree of polarization and azimuth angle are also presented to get a better understanding of the polarization effect. The measurements were done with a dual rotating compensator ellipsometer. The measured wavelength region was from 240 to 1000 nm and the angle of incidence from 25° to 75° in most of the cases. In general very high ellipticities (near circular) are reported. All specimens studied reflect both right- and left-handed polarized light. Depending on the species, two general types of polarization behaviour were observed. Chrysina macropus and Chrysina peruviana showed m41 values close to 0. Green stripes on Chrysina gloriosa showed similar polarization behaviour whereas gold stripes on the same beetle had much more pronounced m41 variations. Large m41 variations were also observed for Chrysina argenteola, Chrysina chrysargyrea and Chrysina resplendens. Four specimens of Chrysina resplendens show different m41 patterns suggesting differences in their structures.

Light reflected from the scarab beetles Cetonia aurata (C. aurata) and Chrysina gloriosa (C. gloriosa) has left-handed polarization. In this work the polarizing properties and structural characteristics of the cuticles of these two beetles are investigated with two different techniques: scanning electron microscopy (SEM) and Mueller-matrix spectroscopic ellipsometry (MMSE). SEM is used to get cross section images of the epicutucle and the endocuticle. Thicknesses around 18 μm were measured for both layers for C. aurata and between 12 and 16 μm for C. gloriosa. A layered structure is observed in both beetles. In addition, a cusp-like structure is also observed in C. gloriosa. MMSE showed left-handed near-circular polarization of light reflected on both beetles. For C. aurata this is observed in a narrow wavelength range (500-600 nm) and for C. gloriosa in a wider wavelength range (400-700 nm) when measured on golden areas of the cuticle. C. gloriosa also has green areas where the reflected light was linearly polarized. The results are used in regression modelling. A good model approximation was found for C. aurata for angles up to 60 whereas a good starting point for future work was reached for C. gloriosa.

Complex surface structures in nature often have remarkable optical properties. By understanding the origin of these properties, such structures may be utilized in metamaterials, giving possibilities to create materials with new specific optical properties. To simplify the optical analysis of these naturally developed surface structures there is a need to assist data analysis and analytical calculations with numerical calculations. In this work an application tool for numerical calculations of optical properties of surface structures, such as reflectances and ellipsometric angles, has been developed based on finite element methods (FEM). The data obtained from the application tool has been verified by comparison to analytical expressions in a thorough way, starting with reflection from the simplest of interfaces stepwise increasing the complexity of the surfaces. The application tool were developed within the electromagnetic module of Comsol Multiphysics and used the script language to perform post-process calculations on the obtained electromagnetic fields. The data obtained from this application tool are given in such way that easily allows for comparison with data received from spectroscopic ellipsometry measurements.

In this work, a gradient of interpenetrating polymer networks, consisting of anionic and cationic polymers, has been investigated with respect to protein resistant properties and swelling characteristics at different pH and ionic strength conditions. The swelling and protein adsorption have been studied using \emph{in situ} spectroscopic ellipsometry(SE) and imaging surface plasmon resonance(iSPR) respectively. It has been shown that, by altering the buffer pH, the region of lowest protein adsorption on the surface could be moved laterally. The swelling has similarly been shown to respond to both changes in pH and ionic strength. Additionally, the arise of surface charge and the polymer swelling in solution, both a consequence of the ionisation of fixed charges on the polymer, have been indicated to occur at different buffer pH. The studied polymer systems show promising properties for future applications in, for example, the biosensor area, where the surface chemistry can be tailor-made to work optimally in a given environment.

Die glasartige Dynamik in nanoskaligen Polymergeometrien ist ein hochaktuelles Forschungsgebiet, dessen Komplexität durch zahlreiche kontroverse Ergebnisse in der Fachliteratur unterstrichen wird. Die vorliegende Dissertation liefert zu dieser Thematik einen fundierten experimentellen Beitrag, indem erstmals an identisch präparierten Polymerfilmen mittels Kombination unterschiedlicher Analysemethoden (Ellipsometrie, Breitband Dielektrischer Spektroskopie, Röntgenreflektometrie) die Glasübergangstemperatur (Tg) in begrenzter Geometrie dünner Filme bestimmt wurde. Folgende Aspekte, die zum Verständnis der glasartigen Dynamik in dünnen Filmen dienen, werden in dieser Arbeit aufgegriffen: I) Welchen Einfluss haben attraktive, repulsive Grenzflächenwechselwirkungen zwischen Polymer und Substrat; II) Welche Rolle spielt die Polymerarchitektur (linear, verzweigt, hochverzweigt); III) Zeigen unterschiedliche Analysemethoden vergleichbare Ergebnisse und IV) In welcher Weise beeinflussen präparative und experimentelle Faktoren den Glasübergang in dünnen Filmen.

For the development of smart surfaces high attention is focused on stimuli-responsive polymers. Since type and rate of response to environmental stimuli can be regulated by chain length, composition, architecture and topology, polymer films offer a variety of opportunities to develop such stimuli-responsive surfaces. Here polymer brush surfaces designed for a controlled adsorption of proteins and a switchable activity of immobilized enzymes are presented. The work is focused on temperature as well as pH-sensitive binary brushes, consisting of poly(N-isopropylacrylamide) (PNIPAAm) and poly(acrylic acid) (PAA), and their swelling behavior as well as their protein adsorption affinity is compared to the corresponding homopolymer brushes. All polymer brushes are covalently grafted by ester bonds to an anchoring layer of poly(glycidyl methacrylate), that itself is grafted via ether bonds to a silicon surface. Methodical investigations of layer thickness and refractive index of the brushes in the swollen state and after protein adsorption are carried out with in-situ spectroscopic ellipsometry, varying the brush composition and the solution parameters pH, salt concentration and temperature. The ellipsometric findings are correlated to results of contact angle, atomic force microscopy and zeta-potential measurements as well as colorimetric assays of enzyme activities at the brush surface. Furthermore the swelling of PNIPAAm brushes and protein adsorption at PAA Guiselin brushes are investigated in more detail with attenuated total reflexion Fourier-transform infrared spectroscopy and quartz crystal microbalance with dissipation, respectively.

A novel lithographic fabrication method is used to fabricate nanopillars arrays of anisotropic Ag and TCO electrodes. Optical and electrical properties of the electrodes including bandgap, free carrier concentration, resistivity and surface plasmon frequency of different electrodes can be tuned by adjusting the dimensions and geometry of the pillars. Given the ability to tune the nonlocal responses of the plasmonic field enhancements, we attempt to determine the nature of the effective refractive index profile within the visible wavelength region for multi-layer hybrid nanostructures. Knowledge of the effective optical constants of the obtained structure is critical for various applications. nanopillars of TCO\Ag core shell structures have been successfully fabricated. The Maxwell-Garnett mixing law has been used to determine the optical constants of the nanostructure based on spectroscopic ellipsometry measurements. Simulated reflection spectra indicate a down shift in the Brewster angle of the pillars resulting from the reduction in the effective refractive index of the nanostructure. Two plasmonic resonances were observed, with one in the visible region and the other in the IR region. Plasmon hybridization model is used to describe the behavior of metal and metal oxide core shell nanostructured electrodes. Different charge density distributions around the pillars determine the plasma frequency which depends on the core and surrounding media dielectric constants. Finite Difference Time Domain (FDTD) simulation of different structures agree well with experiment and help us to understand electric field behavior at different structures with different geometries and dielectric constants. Plasmonic Ag nanopillar arrays are effective substrates for surface enhanced Raman spectroscopy (SERS). An enhancement factor up to 6 orders of magnitude is obtained. Monolayers of C60 is deposited on the Ag nanopillars and the interface of C60/Ag is studied which is important in optoelectronic devices. Electron delocalization between C60 and Ag is confirmed.