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This chapter is mainly a review of research done by the author, concerning theory of surface plasmon resonance interaction with fluorophores. Surface plasmon coupled emission (SPCE) is studied theoretically and compared to experiment. Surface plasmon resonance optical field enhancement is investigated at elongated particles by solving the Maxwell’s equations with the use of spheroidal vector wave functions. Finally, the theoretical possibility of trapping fluorophores by optical gradient forces at surface plasmon enhanced hot spots is examined.

Enhanced understanding of the chemistry of aminothiols promotes both the development of novel chemosensors and new insights into their biochemistry.

In this article, I have given an overview of the application of microparticle-based flow cytometry to high resolution molecular analysis. The applications described range from kinetic analysis of interaction mechanisms to highly sensitive and parallel screening assays. Some of these types of applications are now widely used, supported by commercial kits and reagents. Others are being integrated into high throughput screening environments for disease marker and drug discovery. Current research in new optical encoding schemes for microparticles, new detection schemes for fluorescence and other optical signals, and microparticle fabrication and surface chemistries promise to lead to even more flexible and robust assay systems for molecular analysis

The combination of total internal reflection illumination with fluorescence correlation spectroscopy (TIR-FCS) is an emerging technique. This method allows measurement of at least three key properties of fluorophores very close to surface/solution interfaces, including the local fluorophore concentration, the local fluorophore translational mobility, and the kinetic rate constants which describe the reversible association of fluorophores with the interface. This review describes the conceptual basis of TIR-FCS, aspects important to the experimental realization of this technique, and methods for theoretically modeling and analyzing data. Previous experimental applications of TIR-FCS are also summarized, including studies of protein dynamics very close to substrate-supported planar membranes, measurement of the kinetic dissociation rate for fluorescent ligands specifically and reversibly associating with receptors in substrate-supported planar membranes, the interaction of small dye molecules with chromatographic surfaces, investigations of fluorophore behavior in sol-gel films, and the monitoring of intracellular vesicular motion near the inner leaflet of plasma membranes in intact, live cells. A number of potential future directions for TIR-FCS are indicated, for example, the use of very high refractive index substrates or small, metallic substrate-deposited structures, the use of photon counting histograms, the use of a single fluorescent reporter molecule to provide kinetic rate constants for nonfluorescent molecules which compete for the same surface sites, and more sophisticated methods of data analysis including two-color cross-correlation and high-order autocorrelation.