The in situ measurement of adsorption and immobilization of proteins in liquid cells is a complex task influenced by numerous parameters. Most of these factors (like temperature of the cell, purity of water, rate of injection) are known to have little effect on the repeatability of the measurement (Castro et al., Surf. Sci. 601 [2007] 1795). On the other hand, there are various possible causes of uncertainty that need to be investigated. As an improvement of our standard procedure for protein immobilization (Kozma et al., phys. stat. sol. 5 (2008) 1427), we studied the influence of different substrate materials, including virgin and chemically activated thermal SiO2 and Ta2O5 thin films on Si wafer, in the aspect of the properties of protein adsorption (kinetics, surface coverage and the stability of the deposited material against detergent flow) by ellipsometry and atomic force microscopy. The adsorption of flagellar filaments was investigated using two-layer effective medium models that accounted for the vertical density distribution of the filaments with lengths around 500-1000 nm bound to the surface. We performed measurements also on suprasil/Ta2O5 structures to directly compare the results of ellipsometry with that of optical waveguide lightmode spectroscopy. We also investigated flow cells of different constructions mainly focusing on the capacity. We designed a flow cell with significantly smaller volume for economic measurements and for a better understanding of protein adsorption. The development of the flow cell was supported by finite element flow dynamics calculations. We also made attempts to improve our standard procedure for immobilization with a modified surface treatment, as well as to measure receptor attachment.

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