This dissertation focuses on the development of algorithms for analyzing and modeling of the signals from optical spectroscopy. This dissertation is motivated by the detection of oral cancer, but some of the methods developed can be generalized to epithelial cancers of other sites. Two main topics are covered in this dissertation: Analysis and Modeling. For analysis, the focus is on developing algorithms to make diagnostic predictions. The analysis methods are empirically tested using an oral cancer dataset. Statistical analyses show that polarized reflectance spectroscopy has the potential to aid screening and diagnosis of oral cancer. Also, a novel adaptive windowing technique is developed to extract spectral features with fewer windows that retain the diagnostic information. For modeling, a Monte Carlo model simulating light-tissue interactions is presented to aid in the design of diagnostic instrumentation. / text

The method of dipole orientation of protein complexes using electric fields plays a key role in the development of single particle imaging, since it enables orientation of the protein in vacuum. In the orientation process the protein is exposed to an external electric field along which the dipole axis of the protein will eventually align. Earlier studies using molecular dynamics simulations have implemented a constant electric field to examine the dipole orientation process. However, when injected into the electric field the protein experiences a gradually increasing field strength converging to some terminal field strength rather than a constant electric field. In order to examine the effects of the time-dependant nature of the electric field, in comparison to a constant one, fields with different time dependances were implemented in molecular dynamics simulations in vacuum performed with GROMACS. Ubiquitin was chosen as a model protein. The results of the study show time-increasing fields tend to result in slower orientation, but preserve the structure of the protein better than for a constant field. It was also shown that after 10 ns electric field exposure, with terminal field strengths greater  or equal to 0.6Vnm^-1, there was no apparent difference of the average degree of orientation of proteins within the time-increasing fields and the constant one. However, for fields of greater or equal to 1.5Vnm^-1 the constant field tended to result in a larger change of the protein structure.