Description of atmospheric conditions at the Pierre Auger Observatory using the Global Data Assimilation System (GDAS)

Atmospheric conditions at the site of a cosmic ray observatory must be known for reconstructing observed extensive air showers. The Global Data Assimilation System (GDAS) is a global atmospheric model predicated on meteorological measurements and numerical weather predictions. GDAS provides altitude-dependent profiles of the main state variables of the atmosphere like temperature, pressure, and humidity. The original data and their application to the air shower reconstruction of the Pierre Auger Observatory are described. By comparisons with radiosonde and weather station measurements obtained on-site in Malargue and averaged monthly models, the utility of the GDAS data is shown. (C) 2012 Elsevier B.V. All rights reserved.

Resonances in Mie scattering by an inhomogeneous atomic cloud

Despite the quantum nature of the process, collective scattering by dense cold samples of two-level atoms can be interpreted classically describing the sample as a macroscopic object with a complex refractive index. We demonstrate that resonances in Mie theory can be easily observable in the cooperative scattering by tuning the frequency of the incident laser field or the atomic number. The solution of the scattering problem is obtained for spherical atomic clouds who have the parabolic density characteristic of BECs, and the cooperative radiation pressure force calculated exhibits resonances in the cloud displacement for dense clouds. At odds with uniform clouds which show a complex structure including narrow peaks, these densities show resonances, yet only under the form of quite regular and contrasted oscillations. Copyright (C) EPLA, 2012

EVAPORATIVE LIGHT-SCATTERING DETECTOR FOR ANALYSIS OF NATURAL PRODUCTS

EVAPORATIVE LIGHT-SCATTERING DETECTOR FOR ANALYSIS OF NATURAL PRODUCTS. The interest in the use of evaporative light scattering detector (ELSD) for the analysis of different classes of natural products has grown over the years. This is because this detector has become an excellent alternative compared to other types of detectors, such as the refractive index detector and the ultraviolet (UV) detector. This review describes the basic principles of ELSD functioning and discusses the advantages and disadvantages in using an ELSD for the analysis of organic compounds. Additionally, an overview, covering the last 23 years, of ELSD applications in natural products analysis (saponins, terpenes, carbohydrates, glycosides, alkaloids, steroids, flavonoids, peptides, polyketides, coumarins and iridoids) is presented and discussed.

Transverse pseudo-nonlinear effects measured in solid-state laser materials using a sensitive time-resolved technique

We present a detailed study of the Baryscan technique, a new efficient alternative to the widespread Z-scan technique which has been demonstrated [Opt. Lett. 36:8, 2011] to reach among the highest sensitivity levels. This method is based upon the measurement of optical nonlinearities by means of beam centroid displacements with a position sensitive detector and is able to deal with any kind of lensing effect. This technique is applied here to measure pump-induced electronic refractive index changes (population lens), which can be discriminated from parasitic thermal effects by using a time-resolved Baryscan experiment. This method is validated by evaluating the polarizability variation at the origin of the population lens observed in the reference Cr3+:GSGG laser material.

Utilização de detecção por espalhamento de luz evaporativo para a análise de produtos naturais

The interest in the use of evaporative light scattering detector (ELSD) for the analysis of different classes of natural products has grown over the years. This is because this detector has become an excellent alternative compared to other types of detectors, such as the refractive index detector and the ultraviolet (UV) detector. This review describes the basic principles of ELSD functioning and discusses the advantages and disadvantages in using an ELSD for the analysis of organic compounds. Additionaly, an overview, covering the last 23 years, of ELSD applications in natural products analysis (saponins, terpenes, carbohydrates, glycosides, alkaloids, steroids, flavonoids, peptides, polyketides, coumarins and iridoids) is presented and discussed.

Überkritisches Kohlendioxid als Reaktionsmedium für die Dispersionspolymerisation

Überkritisches Kohlendioxid (CO2) ist für die Polymerisation von besonderem Interesse. Die Dispersionspolymerisation von N-Vinylpyrrolidon (VP) wurde mit Polystyrol-Polydimethylsiloxan Diblockcopolymeren (PS-b-PDMS) in diesem Medium durchgeführt. Hierfür wurde ein neues Hochdrucklabor eingerichtet, eine Sichtzelle und eine neuartige Lichtstreuzelle konstruiert. Für die Durchführung von Lichtstreuexperimenten wurde der Brechungs-index von CO2 bis zu hohen Dichten an einer Reflexionsapparatur bestimmt. Mittels dynamischen Lichtstreumessungen an Polydimethylsiloxan (PDMS) in überkritischem CO2 wurden unter den untersuchten Bedingungen ein Radius bestimmt, wie er für ungestörte Knäueldimensionen erwartet wurde. Das PS-b-PDMS wurde mittels anionischer Polymerisation mit verschiedenen Blocklängen und sehr engen Molekulargewichtsverteilungen synthetisiert. Das Phasenverhalten von PS-b-PDMS wurde in überkritischem CO2 visuell und in einer VP/CO2-Mischung mittels Turbidimetrie untersucht. Das Monomer wirkt als Co-Solvens für den PDMS-Block des Stabilisators. Bei einer Konzentration von ca. 1 Gew.-% PS-b-PDMS (pro Monomer) in CO2 bei 38 MPa und 80°C wurden sphärische ca. 1µm große PVP-Partikeln synthetisiert. PS-b-PDMS ist unter diesen Bedingungen ein geeigneter Stabilisator für die Polymerisation von VP in überkritischem CO2. Bei Konzentrationen von mehr als ca. 5 Gew.-% PS-b-PDMS wurden agglomerierte Partikeln beobachtet. Die Kinetik der Partikelentstehung wurde turbidimetrisch untersucht. Bereits in der frühen Phase der Polymerisation wurde eine anwachsende Partikelgröße gefunden.

Charakterisierung und Stabilität von Arthropoden-Hämocyanin

Hämocyanine sind große, multimere Sauerstofftransport- proteine, die frei gelöst in der Hämolymphe von Arthropoden und Mollusken vorkommen.Zur Charakterisierung verschiedener Arthropoden-hämocyanine wurden deren molare Massen bestimmt. Die mit einer Vielwinkel-Laser-Lichtstreuapparatur ermittelten Molekulargewichte zeigten eine grosse Schwankungsbreite. Dies konnte auf Ungenauigkeiten der zur Berechnung der Molekulargewichte verwendeten spezifischen Extinktions- koeffizienten und Brechungsindex-Inkremente zurückgeführt werden.Mit der Methode der Massenspektrometrie (MALDI-TOF) bestimmte Molekulargewichte einzelner Untereinheiten des Hämocyanins der Vogelspinne Eurypelma californicum zeigten eine sehr gute Übereinstimmung mit aus der Sequenz errechneten Werten.Für das 24-mere Spinnenhämocyanin von Eurypelma californicum wurde die Stabilität gegenüber GdnHCl und der Temperatur auf den verschiedenen strukturellen Ebenen des Proteins untersucht.Viele Stabilitätsuntersuchungen werden an kleinen Proteinen durchgeführt, deren Entfaltung kooperativerfolgt. Bei größeren Proteinen mit unterschiedlichen strukturellen Bereichen (Domänen) ist der Entfaltungs-prozess weitaus komplexer. Ziel war es, durch die Denaturierung des Spinnen-Hämocyanins Erkenntnisse über die Stabilität und Entfaltung der verschiedenen strukturellen Ebenen eines so großen Proteinkomplexes zu gewinnen.Ein wichtiges Charakteristikum für die Interpretation der Entfaltungsexperimente ist die starke Löschung der Tryptophanfluoreszenz im oxygenierten Spinnen-Hämocyanin. Die Löschung kann vollständig durch Förster-Transfer erklärt werden kann. Sie bleibt auf die einzelnen Untereinheiten beschränkt und stellt somit ein reines O₂-Beladungssignal dar.Unter Einwirkung von GdnHCl dissoziiert das native, 24-mere Spinnen-Hämocyanin ohne die Entstehung langlebiger Inter- mediate. Die Untereinheiten werden durch das Oligomer stabilisiert. Die Entfaltung eines Monomers, der Unter- einheit e, folgt einer Hierarchie der verschiedenen strukturellen Ebenen des Moleküls. Die Entfaltung beginnt zunächst von außen mit der Auflockerung der Tertiärstruktur. Der Kern von Domäne II mit dem aktiven Zentrum weist hingegen eine besondere Stabilität auf.Die ausgeprägte Hitzestabilität des Eurypelma-Hämocyanins hängt vom Oligomerisierungsgrad, dem verwendeten Puffer und dessen Ausgangs-pH-Wert ab und spiegelt offensichtlich die extremen Lebensbedingungen im Habitat wider.

Simulative Investigation on the Electronic, Vibrational and Optical Properties of the Ge2Sb2Te5 Chalcogenide

Chalcogenides are chemical compounds with at least one of the following three chemical elements: Sulfur (S), Selenium (Sn), and Tellurium (Te). As opposed to other materials, chalcogenide atomic arrangement can quickly and reversibly inter-change between crystalline, amorphous and liquid phases. Therefore they are also called phase change materials. As a results, chalcogenide thermal, optical, structural, electronic, electrical properties change pronouncedly and significantly with the phase they are in, leading to a host of different applications in different areas. The noticeable optical reflectivity difference between crystalline and amorphous phases has allowed optical storage devices to be made. Their very high thermal conductivity and heat fusion provided remarkable benefits in the frame of thermal energy storage for heating and cooling in residential and commercial buildings. The outstanding resistivity difference between crystalline and amorphous phases led to a significant improvement of solid state storage devices from the power consumption to the re-writability to say nothing of the shrinkability. This work focuses on a better understanding from a simulative stand point of the electronic, vibrational and optical properties for the crystalline phases (hexagonal and faced-centered cubic). The electronic properties are calculated implementing the density functional theory combined with pseudo-potentials, plane waves and the local density approximation. The phonon properties are computed using the density functional perturbation theory. The phonon dispersion and spectrum are calculated using the density functional perturbation theory. As it relates to the optical constants, the real part dielectric function is calculated through the Drude-Lorentz expression. The imaginary part results from the real part through the Kramers-Kronig transformation. The refractive index, the extinctive and absorption coefficients are analytically calculated from the dielectric function. The transmission and reflection coefficients are calculated using the Fresnel equations. All calculated optical constants compare well the experimental ones.

High pressure surface plasmon spectroscopy

Der Einfluß von Druck auf die Eigenschaften dünner dielektrischer Filme wurde mit Hilfe von Oberflächenplasmonen-Spektroskopie untersucht. Die Arbeit kann aus der Perspektive der Materialcharakterisierung und aus apparativer Sicht betrachtet werden, da z.B. eine neue Hochdruckzelle konstruiert wurde, die kombinierte Oberflächenplasmonen-Elektrochemie Messungen erlaubt. SiO2-Solgel Filme wurden optimiert und auf ihre Widerstandsfähigkeit in Bufferlösungen und ihre Oberflächeneigenschaften hin untersucht. Eine Anwendung lag in der Charakterisierung von thermoresponsiven Acrylsäureisopropylamid Hydrogelen, die einen Volumenphasenübergang aufwiesen, dessen Eigenschaften durch Druck und die Beschränktheit des Films auf die Oberfläche beeinflußt wurden.Die Charakterisierung von DNA Hybridisierungsreaktionen an Oberflächen wurde mit einer Fluoreszenz-erweiterten Hochdruckapparatur durchgeführt. Zunächst wurde die Stabilität der zugrundeliegenden Bindematrix sichergestellt. Bei DNA Einzelsträngen führten Temperatur und Druck zu jeweils verringertem bzw. erhöhtem Signal. Entropie und Änderungen der Lösungsmitteleigenschaften wurden für die Signaländerungen verantwortlich gemacht. Die Eigenschaften der Doppelhelix wurden im Langmuir-Bild beschrieben. Der Brechungsindex von Kohlendioxid wurde bis zu 200 MPa gemessen und mit vorhandenen Gleichungen verglichen. Weiterhin wurde das Schwellverhalten von PMMA in scCO2/MMA-Mischungen untersucht. Mit Druck und MMA-Konzentration nimmt das Polymer vermehrt Kohlendioxid auf. Dadurch schwillt es an und sein Brechungsindex nimmt ab. Berechnungen unter Annahme einer idealen Mixtur ergaben gute qualitative Übereinstimmung mit den Meßwerten.Abschließend wurde eine neue Elektrochemie-Hochdruckzelle vorgestellt, die an Kaliumhexacyanoferrat(III)-(II) getestet wurde. Die Elektropolymerisation von Thiophen optisch untersucht.

Chemical and physical properties of Amazonian aerosol particles

- ZUSAMMENFASSUNG:Die vorliegende Dissertation befasst sich mit der Bestimmung der chemischen und physikalischen Eigenschaften von Aerosolpartikeln im Amazonasbecken, die während Zeiten mit Biomasseverbrennung und bei Hintergrundbedingungen bestimmt wurden. Die Messungen wurden während zwei Kampagnen im Rahmen des europäischen Beitrags zum LBA-EUSTACH Experiment in Amazonien. Die Daten umfassen Messungen der Anzahlkonzentrationen, Größenverteilungen, optischen Eigenschaften sowie Elementzusammensetzungen und Kohlenstoffgehalte der gesammelten Aerosole. Die Zusammensetzung des Aerosols wies auf folgende drei Quellen hin: natürlichen biogenen, Mineralstaub, und pyrogenes Aerosol. Aller drei Komponenten trugen signifikant zur Extinktion des Sonnenlichts bei. Insgesamt ergab sich eine Steigerung der Meßwerte um ca. das Zehnfache während der Trockenzeit im Vergleich zur Regenzeit, was auf eine massive Einbringung von Rauchpartikeln im Submikrometerbereich in die Atmosphäre während der Trockenzeit zurückzuführen ist. Dementsprechend sank die Einzelstreualbedo von ca. 0,97 auf 0,91. Der Brechungsindex der Aerosolpartikel wurde mit einer neuen iterative Methoden, basierend auf der Mie-Theorie berechnet. Es ergaben sich durchschnittliche Werte von 1,42 – 0,006i für die Regenzeit und 1,41 – 0,013i für die Trockenperiode. Weitere klimatisch relevante Parameterergaben für Hintergrundaerosole und für Aerosole aus Biomasseverbrennung folgende Werte: Asymmetrieparameter von 0,63 ± 0,02 bzw. 0,70 ± 0,03 und Rückstreuungsverhältnisse von 0,12 ± 0,01 bzw. 0,08 ± 0,01. Diese Veränderungen haben das Potential, das regionale und globale Klima über die Variierung der Extinktion der Sonneneinstrahlung als auch der Wolkeneigenschaften zu beeinflussen.

Modeling of complex chemical reactions and macromolecular orientation phenomena in confined geometries

The cooperative motion algorithm was applied on the molecular simulation of complex chemical reactions and macromolecular orientation phenomena in confined geometries. First, we investigated the case of equilibrium step-growth polymerization in lamellae, pores and droplets. In such systems, confinement was quantified as the area/volume ratio. Results showed that, as confinement increases, polymerization becomes slower and the average molecular weight (MW) at equilibrium decreases. This is caused by the sterical hindrance imposed by the walls since chain growth reactions in their close vicinity have less realization possibilities. For reactions inside droplets at surfaces, contact angles usually increased after polymerization to compensate conformation restrictions imposed by confinement upon growing chains. In a second investigation, we considered monodisperse and chemically inert chains and focused on the effect of confinement on chain orientation. Simulations of thin polymer films showed that chains are preferably oriented parallel to the surface. Orientation increases as MW increases or as film thickness d decreases, in qualitative agreement with experiments with low MW polystyrene. It is demonstrated that the orientation of simulated chains results from a size effect, being a function of the ratio between chain end-to-end distance and d. This study was complemented by experiments with thin films of pi-conjugated polymers like MEH-PPV. Anisotropic refractive index measurements were used to analyze chain orientation. With increasing MW, orientation is enhanced. However, for MEH-PPV, orientation does not depend on d even at thicknesses much larger than the chain contour length. This contradiction with simulations was discussed by considering additional causes for orientation, for instance the appearance of nematic-like ordering in polymer films. In another investigation, we simulated droplet evaporation at soluble surfaces and reproduced the formation of wells surrounded by ringlike deposits at the surface, as observed experimentally. In our simulations, swollen substrate particles migrate to the border of the droplet to minimize the contact between solvent and vacuum, which costs the most energy. Deposit formation in the beginning of evaporation results in pinning of the droplet. When polymer chains at the substrate surface have strong uniaxial orientation, the resulting pattern is no longer similar to a ring but to a pair of half-moons. In a final stage, as an extension for the model developed for polymerization in nanoreactors, we studied the effect of geometrical confinement on a hypothetical oscillating reaction following the mechanism of the so called periodically forced Brusselator. It was shown that a reaction which is chaotic in the bulk may be driven to periodicity by confinement and vice-versa, opening new perspectives for chaos control.

New platforms for optical biosensing

Physicochemical experimental techniques combined with the specificity of a biological recognition system have resulted in a variety of new analytical devices known as biosensors. Biosensors are under intensive development worldwide because they have many potential applications, e.g. in the fields of clinical diagnostics, food analysis, and environmental monitoring. Much effort is spent on the development of highly sensitive sensor platforms to study interactions on the molecular scale. In the first part, this thesis focuses on exploiting the biosensing application of nanoporous gold (NPG) membranes. NPG with randomly distributed nanopores (pore sizes less than 50 nm) will be discussed here. The NPG membrane shows unique plasmonic features, i.e. it supports both propagating and localized surface plasmon resonance modes (p SPR and l-SPR, respectively), both offering sensitive probing of the local refractive index variation on/in NPG. Surface refractive index sensors have an inherent advantage over fluorescence optical biosensors that require a chromophoric group or other luminescence label to transduce the binding event. In the second part, gold/silica composite inverse opals with macroporous structures were investigated with bio- or chemical sensing applications in mind. These samples combined the advantages of a larger available gold surface area with a regular and highly ordered grating structure. The signal of the plasmon was less noisy in these ordered substrate structures compared to the random pore structures of the NPG samples. In the third part of the thesis, surface plasmon resonance (SPR) spectroscopy was applied to probe the protein-protein interaction of the calcium binding protein centrin with the heterotrimeric G-protein transducin on a newly designed sensor platform. SPR spectroscopy was intended to elucidate how the binding of centrin to transducin is regulated towards understanding centrin functions in photoreceptor cells.

Polymer properties measured by micromechanical cantilever technique

Surface stress changes induced by specific adsorption of molecules were investigated using a micromechanical cantilever sensor (MCS) device. 16 MCS are grouped within four separate wells. Each well can be addressed independently by different liquid enabling functionalization of MCS separately by flowing different solutions through each well and performing sensing and reference experiments simultaneously. In addition, each well contains a fixed reference mirror, which allows measuring the absolute bending of MCS. The effect of the flow rate on the MCS bending change was found to be dependent on the absolute bending value of MCS. In addition, the signal from the reference mirror can be used to follow refractive index changes upon mixing different solutions. Finite element simulation of solution exchange in wells was compared with experiment results. Both revealed that one solution can be exchanged by another one after a total volume of 200 µl has flown through. Using MCS, the adsorption of thiolated deoxyribonucleic acid (DNA) molecules and 6-mercapto-1-hexanol (MCH) on gold surfaces, and the DNA hybridization were performed. The nanomechanical response is in agreement with data reported by Fritz et al.1 Thus, the multiwell device is readily applicable for sensing of multiple chemical and biological recognition events in a single step. In this context controlled release and uptake of drugs are currently widely discussed. As a model system, we have used polystyrene (PS) spheres with diameters in the order of µm. The swelling behavior of individual PS spheres in toluene vapor was studied via mass loading by means of micromechanical cantilever sensors. For 4–8% cross-linked PS a mass increase of 180% in saturated toluene vapor was measured. In addition, the diameter change in saturated toluene vapor was measured and the corresponding volume increase of 200% was calculated. The mass of the swollen PS sphere decreases with increasing exposure time to ultraviolet (UV) light. The swelling response is significantly different between the first and the second exposure to toluene vapor. This is attributed to the formation of a cross-linked shell at the surface of the PS spheres. Shape persistent parts were observed for locally UV irradiated PS spheres. These PS spheres were found to be fluorescent and cracks occur after exposure in toluene liquid. The diffusion time of dye molecules in PS spheres increases with increasing chemical cross-linking density. This concept of locally dissolving non cross-linked PS from the sphere was applied to fabricate donut structures on surfaces. Arrays of PS spheres were fabricated using spin coating. The donut structure was produced simply after liquid solvent rinsing. The complete cross-linking of PS spheres was found after long exposure time to UV. We found that stabilizers play a major role in the formation of the donut nanostructures.

Plasmons as sensors

“Plasmon” is a synonym for collective oscillations of the conduction electrons in a metal nanoparticle (excited by an incoming light wave), which cause strong optical responses like efficient light scattering. The scattering cross-section with respect to the light wavelength depends not only on material, size and shape of the nanoparticle, but also on the refractive index of the embedding medium. For this reason, plasmonic nanoparticles are interesting candidates for sensing applications. Here, two novel setups for rapid spectral investigations of single nanoparticles and different sensing experiments are presented.rnrnPrecisely, the novel setups are based on an optical microscope operated in darkfield modus. For the fast single particle spectroscopy (fastSPS) setup, the entrance pinhole of a coupled spectrometer is replaced by a liquid crystal device (LCD) acting as spatially addressable electronic shutter. This improvement allows the automatic and continuous investigation of several particles in parallel for the first time. The second novel setup (RotPOL) usesrna rotating wedge-shaped polarizer and encodes the full polarization information of each particle within one image, which reveals the symmetry of the particles and their plasmon modes. Both setups are used to observe nanoparticle growth in situ on a single-particle level to extract quantitative data on nanoparticle growth.rnrnUsing the fastSPS setup, I investigate the membrane coating of gold nanorods in aqueous solution and show unequivocally the subsequent detection of protein binding to the membrane. This binding process leads to a spectral shift of the particles resonance due to the higher refractive index of the protein compared to water. Hence, the nanosized addressable sensor platform allows for local analysis of protein interactions with biological membranes as a function of the lateral composition of phase separated membranes.rnrnThe sensitivity on changes in the environmental refractive index depends on the particles’ aspect ratio. On the basis of simulations and experiments, I could present the existence of an optimal aspect ratio range between 3 and 4 for gold nanorods for sensing applications. A further sensitivity increase can only be reached by chemical modifications of the gold nanorods. This can be achieved by synthesizing an additional porous gold cage around the nanorods, resulting in a plasmon sensitivity raise of up to 50 % for those “nanorattles” compared to gold nanorods with the same resonance wavelength. Another possibility isrnto coat the gold nanorods with a thin silver shell. This reduces the single particle’s resonance spectral linewidth about 30 %, which enlarges the resolution of the observable shift. rnrnThis silver coating evokes the interesting effect of reducing the ensemble plasmon linewidth by changing the relation connecting particle shape and plasmon resonance wavelength. This change, I term plasmonic focusing, leads to less variation of resonance wavelengths for the same particle size distribution, which I show experimentally and theoretically.rnrnIn a system of two coupled nanoparticles, the plasmon modes of the transversal and longitudinal axis depend on the refractive index of the environmental solution, but only the latter one is influenced by the interparticle distance. I show that monitoring both modes provides a self-calibrating system, where interparticle distance variations and changes of the environmental refractive index can be determined with high precision.

New biosensor applications of surface plasmon and hydrogel optical waveguide spectroscopy

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