<p>Cancer is a disease that affects millions of people each year. While methods for the prevention and treatment of the disease continue to advance, the early detection of precancerous development remains a key factor in reducing mortality and morbidity among patients. The current gold standard for cancer detection is the systematic biopsy. While this method has been used for decades, it is not without limitations. Fortunately, optical detection of cancer techniques are particularly well suited to overcome these limitations. This dissertation chronicles the development of one such technique called Fourier domain low coherence interferometry (fLCI). </p><p>The presented work first describes a detailed analysis of temporal and spatial coherence. The study shows that temporal coherence information in time frequency distributions contains valuable structural information about experimental samples. Additionally, the study of spatial coherence demonstrates the necessity of spatial resolution in white light interferometry systems. The coherence analysis also leads to the development of a new data processing technique that generates depth resolved spectroscopic information with simultaneously high depth and spectral resolution. </p><p>The development of two new fLCI optical systems is also presented. These systems are used to complete a series of controlled experiments validating the theoretical basis and functionality of the fLCI system and processing methods. First, the imaging capabilities of the fLCI system are validated through scattering standard experiments and animal tissue imaging. Next, the new processing method is validated by a series of absorption phantom experiments. Additionally, the nuclear sizing capabilities of the fLCI technique are validated by a study measuring the nuclear morphology of in vitro cell monolayers.</p><p>The validation experiments set the stage for two animal studies: an initial, pilot study and a complete animal trial. The results of these animal studies show that fLCI can distinguish between normal and dyplastic epithelial tissue with high sensitivity and specificity. The results of the work presented in this dissertation show that fLCI has great potential to develop into an effective method for early cancer detection.</p> / Dissertation

Protein crystallization is significant in both biotechnology and biomedical applications. In biotechnology, crystallization is essential for determining the structure of both native and synthesized therapeutically important proteins. It can also be used as a final purification step and as a stable form for protein storage. With regard to biomedical systems, protein crystallization appears to be involved in the development and manifestation of certain human diseases. In particular, there exists evidence that L-rich ferritin crystals are involved in Hereditary Hyperferritinemia Cataract Syndrome (HHCS). In the current research a microbatch crystallization apparatus has been introduced that enables (1) multiple batch crystallization experiments at various temperatures and solution conditions in parallel and (2) quantitative monitoring of crystal growth without disturbing the progress of an experiment for observation. The primary application of the apparatus is, but not limited to, screening of protein crystallization conditions, although the system can also be used for other macromolecular and small-molecule crystallization experiments. Multiwell microbatch experiments demonstrated the dependence of apoferritin crystal growth kinetics and final crystal size on temperature and cadmium concentration. Although the solubility of apoferritin might be independent of temperature, the results of this study show that the crystal growth kinetics are affected by temperature, profoundly under some conditions. For apoferritin under near physiological conditions the solution thermodynamics in the form of the second virial coefficient have proofed to be a valuable predictor for the crystallization outcome. Furthermore, the significance of the elevated level of some divalent cations in cataractous lenses has been studied both in dilute solutions and under crystallization conditions and cadmium seems to be sole menace in apoferritin condensation.

The study proposed a high efficient dye sensitize solar cell (DSSC) by embedding liquid crystal in liquid electrolyte. When liquid crystal molecules was disperse in the liquid electrolyte, the light-scattering occur due to refractive index mismatching by randomly oriented liquid crystal droplets. The light-scattering allows solar light have longer optical path length within the solar cell and therefore enhances light-trapping efficiency of N719 dye. The experiment results reveal that the DSSC with the liquid crystal concentration of 20 wt% have best electric conversion efficiency. Moreover, the study also introduces chloseteric liquid crystal to the liquid electrolyte of a DSSC and compare with nematic liquid crystal embedded DSSC. The cholesteric liquid crystal with periodic helical structure in the liquid electrolyte provides not only light-scattering but also selective reflection. Compared with nematic liquid crystal embedded DSSC, the cholesteric liquid crystal embeded DSSC has a more large light-trapping efficiency due to combined effects of light scattering and selective reflection. Besides, when the reflective band (480~580nm) of cholesteric liquid crystal is matched to the absorption spectrum of N719 dye, the DSSC has better photoexcitation of dye and photovoltaic performance.

Predominance of small dense Low Density Lipoprotein (LDL) is associated with a two to threefold increase in risk for Coronary Heart Disease (CVD). Small, dense HDL (High Density Lipoprotein) particles protect small dense LDL from oxidative stress. Technological advancements have introduced an array of techniques for measuring diameters of LDL and HDL as well as estimating overall particle heterogeneity. However, there is lack of comparative studies between these techniques, and, hence, no conclusive evidence to establish the merits of one method relative to others. The primary purpose of this study was to compare Nondenaturing Gradient Gel Electrophoresis (NDGGE) and Dynamic Laser Light Scattering (DLLS) methods in determining LDL and HDL particle diameter. Our comparison entailed: 1) Evaluating the two methods in terms of their reproducibility 2) Correlating the two methods(in future studies method selection would be driven by time and cost considerations if the two methods correlate), and 3) Evaluating the two methods in terms of their ability to identify bi-modal samples. A secondary purpose of this research was to investigate the effect of refrigerated plasma storage on particle diameter. Reproducibility was measured as Coefficient of Variance (CV). Within and between runs, CV for LDL and HDL for NDGGE were <6% and <15%, respectively and for DLLS, CV within runs were <3% and <5.5%, respectively. No correlation was observed between LDL diameter from the two methods. NDGGE showed two bands for 157 HDL samples of which only 24 samples showed bimodal peaks in DLLS. In order to study the effect of storage, three sample sets of LDL and two sample sets of HDL were used. NDGGE showed a significant difference between mean diameter of fresh and stored LDL and HDL sample for all sets, whereas DLLS showed a significant difference in only one LDL sample set and none for HDL sample sets. We conclude that DLLS may be a better method for measuring LDL diameter because NDGGE overestimated LDL diameter. However, NDGGE was able to resolve subpopulation better in an HDL sample than DLLS. Thus, NDGGE may be a better choice for measuring HDL diameter than DLLS.

The first part of this study is focused on numerical studies of light scattering from a single microscopic particle using the Discrete Dipole Approximation (DDA) method. The conventional DDA formalism is generalized to two cases: (a) inelastic light scattering from a dielectric particle and (b) light scattering from a particle with magnetic permeability u /= 1. The first generalization is applied to simulations of Raman scattering from bioaerosol particles, and the second generalization is applied to confi rmation of irregular invisibility cloaks made from metamaterials. In the second part, radiative transfer in a coupled atmosphere-ocean system is solved to study the asymptotic nature of the polarized light in deep oceans. The rate at which the radiance and the polarization approach their asymptotic forms in an ideal homogeneous water body are studied. Effects of the single scattering albedo and the volume scattering function are studied. A more realistic water body with vertical pro files for oceanic optical properties determined by a Case 1 water model is then assumed to study the e ffects of wavelength, Raman scattering, and surface waves. Simulated Raman scattering patterns computed from the generalized DDA formalism are found to be sensitive to the distribution of Raman active molecules in the host particle. Therefore one can infer how the Raman active molecules are distributed from a measured Raman scattering pattern. Material properties of invisibility cloaks with a few irregular geometries are given, and field distributions in the vicinity of the cloaked particles computed from the generalized DDA formalism con rm that the designated material properties lead to invisibility. The radiative transfer model calculation in deep oceans suggest that the underwater radiance approaches its asymptotic form more quickly than the polarization does. Therefore, a vector radiative transfer solution is necessary for asymptotic light field studies. For a typical homogeneous water body whose scattering property is characterized by the Petzold phase function, a single scattering albedo of w0 > 0:8 is required in order that the asymptotic regime can be reached before there are too few photons to be detected.

Amyloid fibrils results from a type of ordered polypeptide aggregation that is associated with ailments such as Alzheimer's disease (AD). Annually, millions of people in the United States alone develop and die from AD. Therefore, it is necessary to understand not only the process of amyloid formation, but also the causes of this specific type of aggregation. This study used ABeta(25-35) since it is a fragment of the Alzheimer?s peptide that behaves like the full length peptide found in patients with AD. To study the process of amyloid formation, several methods were used so that a more complete picture of the stepped aggregation process could be realized. Several oligomeric species were detected and described many of which could not have been observed without using the complete battery of methods utilized here. The oligomeric species detected included a novel 'rolled sheet' that appeared to be the immediate precursor of amyloid fibrils, and two supermolecular species that appear after amyloid fibrils were formed. In determining the causes of amyloid formation, two significant discoveries were made. First, by partial sequence randomization, truncation, and Ala scanning mutagenesis, the critical amyloidogenic region of ABeta(25-35) was found to be residues 30-35. This critical core region is important because it is thought to be the region that initiates amyloid formation, therefore knowing the residues involved in the region is a useful tool for developing methods of fibril formation prevention. Second, by inserting all naturally occurring amino acids into position 34 of ABeta(25-35), three distinct classes of variants were observed and the effect of several physiochemical properties on amyloidosis were examined. Hydrophobicity, solubility, and ?-strand propensity were found to affect aggregation to the greatest extent. Also within these two studies, our results suggest that early oligomers are the cytotoxic species as opposed to amyloid fibrils or other larger macromolecular assemblies.

Modeling the single-scattering properties of nonspherical particles in the atmo¬sphere (in particular, ice crystals and dust aerosols) has important applications to climate and remote sensing studies. The first part of the dissertation (Chapters II¬V) reports a combination of exact numerical methods, including the finite-difference time-domain (FDTD), the discrete-dipole-approximation (DDA), and the T-matrix methods, and an approximate method-the physical-geometric optics hybrid (PGOH) method-in the computation of the optical properties of the non-spherical particles in a complete range of size parameters. The major advancements are made on the modeling capabilities of the PGOH method, and the knowledge of the electromag¬netic tunneling effect – a semi-classical scattering effect. This research is important to obtain reliable optical properties of nonspherical particles in a complete range of size parameters with satisfactory accuracy and computational efficiency. The second part (Chapters VI-VII) of the dissertation is to investigate the de¬pendence of the optical properties of ice crystals and mineral dust aerosols in the atmosphere on the spectrum, the particle size and the morphology based on compu¬tational models. Ice crystals in the atmosphere can be classified to be simple regular faceted particles (such as hexagon columns, plates, etc.) and imperfect ice crystals. Modeling of the scattering by regular ice crystals is straightforward, as their morphologies can be easily defined. For imperfect ice crystals, the morphology is quite diverse, which complicates the modeling process. We present an effective approach of using irregular faceted particle to characterize the imperfectness of ice crystals. As an example of application, less-than-unity backscattering color ratio of cirrus clouds is demonstrated and explained theoretically, which provides guidance in the calibra¬tion algorithm for 1.064-µm channel on the Calipso lidar. Dust aerosols have no particular morphology. To develop an approach to modeling the optical properties of realistic dust particles, the principle of using simple shapes (triaxial ellipsoids and nonsymmetric hexahedra) to represent irregular dust particles is explored. Simulated results have been compared with those measured in laboratory for several realistic aerosol samples. Agreement between simulated results and measurement suggests the potential applicability of the two aforementioned aerosol models. We also show the potential impact of the present study to passive and active atmospheric remote sensing and future research works.

Interparticle interactions determine the microstructure, stability, rheology, and optical properties of concentrated colloidal suspensions involved in paint, paper, cosmetic, and pharmaceutical industries, etc. Frequency domain photon migration (FDPM) involves modeling the photon transport in a multiple scattering medium as a diffusion process in order to simultaneously determine isotropic scattering and absorption coefficients from measured amplitude attenuation and phase shift of the propagating photon density wave. Using FDPM, we investigated the impact of electrostatic interaction upon the optical properties and structure of dense charged suspensions. We demonstrated that electrostatic interactions among charged polystyrene latex may significantly affect the light scattering properties and structure of dense suspensions at low ionic strength (<0.06 mM NaCl equivalent) by actual FDPM measurement. We showed that the structure factor models addressing electrostatic interaction can be used to describe the microstructure of charged suspensions and quenched scattering due to electrostatics, and demonstrated that FDPM has the potential to be a novel structure and surface charge probe for dense suspensions. We also showed that the FDPM measured isotropic scattering coefficients may respond to the change in effective particle surface charge, and displayed the potential of using FDPM for probing particle surface charge in concentrated suspensions. We presented that the interference approximation implies a linear relationship between the absorption coefficient and volume fraction of suspension. We illustrated that FDPM measured absorption coefficient varies linearly with suspension volume fraction and affirmed the interference approximation from a perspective of light absorption. The validation of the interference approximation enables us to develop the methodology for estimating absorption efficiencies and imaginary refractive indices for both particles and suspending fluid simultaneously using FDPM. We further demonstrated a novel application of FDPM measured absorption coefficients in determining pigment absorption spectra, and displayed the potential of using FDPM as a novel analytical tool in pigment and paint industry.

This work mainly focuses on signal processing issues related to continuous-wave, polarization-based direct imaging schemes. Here, we present a mathematical framework to analyze the performance of the Polarization Difference Imaging (PDI) and Polarization Modulation Imaging (PMI). We have considered three visualization parameters, namely, the polarization intensity (PI), Degree of Linear Polarization (DOLP) and polarization orientation (PO) for comparing these schemes. The first two parameters appear frequently in literature, possibly under different names. The last parameter, polarization orientation, has been introduced and elaborated in this thesis. We have also proposed some extensions/alternatives for the existing imaging and processing schemes and analyzed their advantages. Theoretically and through Monte-Carlo simulations, we have studied the performance of these schemes under white and coloured noise conditions, concluding that, in general, the PMI gives better estimates of all the parameters. Experimental results corroborate our theoretical arguments. PMI is shown to give asymptotically efficient estimates of these parameters, whereas PDI is shown to give biased estimates of the first two and is also shown to be incapable of estimating PO. Moreover, it is shown that PDI is a particular case of PMI. The property of PDI, that it can yield estimates at lower variances has been recognized as its major strength. We have also shown that the three visualization parameters can be fused to form a colour image, giving a holistic view of the scene. We report the advantages of analyzing chunks of data and bootstrapped data under various circumstances. Experiments were conducted to image objects through calibrated scattering media and natural media like mist, with successful results. Scattering media prepared with polystyrene microspheres of diameters 2.97m, 0.06m and 0.13m dispersed in water were used in our experiments. An intensified charge coupled device (CCD) camera was used to capture the images. Results showed that imaging could be performed beyond optical thickness of 40, for particles with 0.13m diameter. For larger particles, the depth to which we could image was much lesser. An experiment using an incoherent source yielded better results than with coherent sources, which we attribute to the speckle noise induced by coherent sources. We have suggested a harmonic based imaging scheme, which can perhaps be used when we have a mixture of scattering particles. We have also briefly touched upon the possible post processing that can be performed on the obtained results, and as an example, shown segmentation based on a PO imaging result.

Η παρουσία σκόνης στο πλάσμα απασχόλησε ιδιαίτερα τους μελετητές στην εκτέλεση εφαρμογών υψηλής τεχνολογίας και κατασκευής. Η εμφάνιση των σωματιδίων μέσα σε αντιδραστήρες πλάσματος, μόλυνε τα υποστρώματα, μείωνοντας κατά αυτό το τρόπο την παραγωγική διαδικασία και διαταράσοντας με απρόβλεπτους τρόπους το πλάσμα. Ο σχηματισμός και η πυρήνωση των σωματιδίων μέσα στο πλάσμα είχε τεράστιες επιπτώσεις στις βιομηχανίες (οικονομικές κτλ.). Βέβαια με την πάροδο των χρόνων και τις αλλεπάληλες μελέτες που έγιναν οι επιστήμονες κατάφεραν να ελέγξουν αυτό το συνεχή σχηματισμό σωματιδίων. Με τον καιρό, κάποιοι μελετητές εκμεταλεύτηκαν την παρουσία σκόνης και οδηγήθηκαν στην ανάπτηξη νέων προϊόντων. Αυτή είναι η περίπτωση των πολυμορφικών ηλιακών κυττάρων (δηλ. αμορφα υδρογονωμενα ηλιακά κύτταρα με ενσωματωμένους νανοκρυσταλλίτες). Η κατασκευή αυτή έγινε απο την ομάδα του Roca i Cabarrocas του Πολυτεχνείου Ecole στην Γαλλία. Στην παρούσα εργασία θα γίνει η μελέτη σχηματισμού και ανάπτυξης των σωματιδίων στα διάφορα στάδιά τους και θα παρουσιαστούν διάφοροι τρόποι ανίχνευσης αυτών. Σκοπός μας είναι να βρούμε την ακριβή χρονική στιγμή σχηματισμού της σκόνης και να επεμβαίνουμε ώστε να σταματάμε την περαιτέρω ανάπτυξή της. / -