Ellipsometry is very attractive for studies of biolayers including protein layers. First, its thickness resolution is well below 1 nm which is perfect for protein layers as they typically are composed of nm-sized molecules. Second, ellipsometry can be used in any transparent medium, so it can be applied to solid-liquid interfaces where many bioreactions take place. Third, molecules do not have to be labeled, as required for techniques based on fluorescence or radioactivity. One drawback is that it is not analytic if operated in the visible spectral range and in simple applications one primarily measures the optical mass on a surface. However, with high precision spectroscopic ellipsometry, structural information in protein monolayers can be obtained in some cases and chemical analysis can be performed with infrared ellipsometry.

In this report, the use of various types of ellipsometry for studies of protein layers at air/solid and liquid /solid interfaces are reviewed. Among the methods included are spectroscopic, dynamic, internal reflection and imaging ellipsometry. Two examples of methodology for analysis are discussed in some detail. First we observe that in situ studies allow monitoring of the dynamics of protein layer growth. Modeling of layer structure by separation of refractive index and thickness from such in situ data recorded during adsorption of fibrinogen layers is presented as well as strategies for evaluation of surface mass density.

In a second example, a model dielectric function (MDF) concept for protein layers in the UV-VIS-IR spectral range is presented. The MDF contains model parameters like resonance energies and broadenings of vibrational structures, e.g. in the amide bands. Changes in these parameters can be monitored and used to assess the conformational state in the protein layer. As an example, studies of thermally induced degradation of fibrinogen layers are presented.

Finally potential sensor applications based on imaging and dynamic ellipsometry utilizing sub-nm thickness resolution are reviewed. The use of surface-plasmon resonance enhancement to increase resolution of internal reflection ellipsometry to pm in thickness will be discussed.

Ellipsometric porosimetry (EP) relies on monitoring the change in optical properties during vapor adsorption/desorption and has been successfully applied to an array of materials using a variety of adsorbates both in vacuum and at ambient pressures. However, these studies typically avoid the analysis of optically complex systems with strong absorbance or optical anisotropy. Towards this end, a hybrid quartz crystal microbalance/ ellipsometric porosimetry (QCM/EP) technique is being developed to facilitate the study of more complex optical materials and to quantitatively estimate parameters such as porosity, pore size distribution, and surface area. To highlight the power of this hybrid approach thin films of TiO₂ and TiC, have been deposited using reactive ballistic deposition (RBD). RBD provides control over film parameters such as surface area, porosity, pore size, and birefringence through variation of the deposition angle. Combined with the QCM/EP technique these films provide a platform for understanding both novel material properties and the requirements for extracting valid optical constants from anisotropic optical materials.

Using first principles scattering models, we have analyzed the ellipsometric response of surfaces that exhibit a self-affine dependence of surface topography on the lateral scale of measurement. This type of surface roughness is found for a wide variety of real surfaces, including many deposited thin films. The calculations show that when the surface correlation length evaluated from the height-height correlation function or the power spectral density is much smaller than the incident wavelength, a universal behavior is found in the ellipsometric response. Both the amplitude of the reflected fields in the p- and s-polarizations, and the thickness of the EMA layer, depend on the product of the rms surface roughness times the average surface slope. Therefore, the linearity between roughness and the thickness of the EMA layer holds only as long as the average surface slope remains constant. That is the case when the growth obeys the predictions of dynamic scaling theory, i.e., the rms roughness and the correlation length change with time as σ ~ t^β and ξ ∼ t^β/α, where α and β are the roughness and the growth exponents, respectively. Results are presented for different materials whose optical properties cover a broad range from metals to dielectrics. An important consequence of this universality is that the ellipsometric response is mathematically separable into two independent functions, one depending only on the optical properties of the film and the other only on the surface topography.

A major challenge for those utilizing ellipsometry is numerical processing of the measured data. The transcendental, multivalued equations arising from the physics of simple reflection are problematic for the least-squares numerical methods in common use. These early numerical methods require fairly accurate initial estimates, bounding to avoid local minima, and only find solutions at the bottom of a relatively flat numerical topography. Previously we have applied Complex Analysis in the n-k plane to improve visualization of the mathematics and this has led to a growing array of new numerical methods avoiding these difficulties. The work presented here extends these new numerical methods for use beyond transparent substrates to include absorbing substrates. Results show that reflection ellipsometry alone can be sufficient for determination of thin absorbing film thickness and optical properties without the need for additional kinds of measurements.

Numerical processing considering surface layers such as air-formed oxides will also be presented.

Ellipsometry is a valuable tool for general materials characterization but also for optical investigations of complex structures including multilayers, photonic crystals, metamaterials and other artificial materials. The complexity of these kind of structures has during the years promoted the use of spectroscopic, variable angle, generalized and Muller-matrix ellipsometry. In parallel more complex optical models and analysis algorithms have come into use.

Naturally occurring structures may show even higher complexity than artifical structures but with a more narrow range of constituent materials, mainly chitin and various proteins. Many interesting structures are found in insects, especially in butterflies and beetles. Fascinating reflection properties result from intricate photonic structures in their wing scales and cuticles. Currently there is a large interest to explore such functional supramolecular architectures for exploitation in nanotechnology.

Even though the optical properties of natural structures are frequently investigated, ellipsometry rarely has been used to reveal structural and optical properties. In this study, Mueller-matrix spectroscopic ellipsometry is applied in the spectral range of 300 to 1700 nm to investigate structures in the cuticle of Scarab beetles, primarily Cetonia aurata (the rose chafer). The cuticle of Cetonia aurata is green with a metallic look and reflects circular polarized light. It has been suggested that the circular polarization of this metallic gloss is caused by a helical structure in the chitinous cuticle. We find that the circular polarization effect is limited to the narrow spectral range 470-550 nm and for shorter or longer wavelengths the reflection properties are similar to those from a near-dielectric material. Furthermore, the light reflected from Cetonia aurata is left-handed circularly polarized and the beetle thus appears black if viewed through a right-handed circular polarizer. In addition to Mueller-matrix spectroscopic ellipsometry, reflectance and scattering measurements are used to characterize the cuticle of Cetonia aurata. Model calculations and parameterization of the nanostructure employing a heliocoidal structure are discussed.