Browsing by Subject "Spectroscopy"
- Results Per Page
- Sort Options
Item Open Access Development of a Fourier Domain Low Coherence Interferometry Optical System for Applications in Early Cancer Detection(2009) Graf, Robert NicholasCancer 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).
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.
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.
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.
Item Open Access Development of Clinically Translatable Technologies for Optical Image-Guided Breast Tumor Removal Surgery(2014) Fu, Henry Li-weiThe rate of occurrence and number of deaths associated with cancer continues to climb each year despite the continual efforts to battle the disease. When given a cancer diagnosis, it is particularly demoralizing and devastating news to a patient. Generally, cancer is defined as the uncontrolled rapid growth of abnormal cells with metastatic potential. In the cancer types originating from solid tissue or organ sites, a tumor will grow as a result of this rapid proliferation of cells. Surgical resection is a commonly used as part of the treatment regimen prescribed for these types of cancer.
Specifically in breast cancer, which impacts over 200,000 women a year, surgical intervention is used in almost 92% of treated cases. A specific surgical procedure is known as breast conserving surgery (BCS), where the physician removes only the tumor, while retaining as much normal tissue as possible. BCS is used in 59% of cases and is generally more preferable than the more radically mastectomy procedure where the entire breast is removed.
To minimize the chance of local recurrence, it is vital that the tumor is completely removed and residual cancer cells are not still present in the patient. This diagnosis is made by inspecting the edge of the resected tumor mass, typically known as the surgical margin. If tumor cells are still present at the margin, then a positive diagnosis is given and tumor cells likely remain inside the patient. Unfortunately, since margins are typically diagnosed using post-operative pathology a patient with a positive margin must undergo a second re-excision operation to remove additional tissue.
For breast cancer patients undergoing BCS, a staggering 20-70% of patients must undergo additional operations due to incomplete tumor removal during the first procedure.
Currently, there are two intra-operative techniques that are used, frozen section analysis and touch prep cytology. Although both have been proven to be effective in reducing re-excision rates, both techniques require
There remains a clinical unmet need for an intra-operative technology capable of quickly diagnosis tumor margins during the initial surgical operation
Optical technologies provide an attractive method of quickly and non-destructively assessing tissue. These techniques rely the interactions of light with tissue, which include absorption, scattering, and fluorescence. Utilizing proper measurement systems, these interactions can be measured and exploited to yield specific sources of contrast in tissue. In this dissertation, I have focused on developing two specific optical techniques for the purpose of surgical margin assessment.
The first is diffuse reflectance spectroscopy (DRS) which is a specific method to extract quantitative biological composition of tissues has been used to discern tissue types in both pre-clinical and clinical cancer studies. Typically, diffuse reflectance spectroscopy systems are designed for single-point measurements. Clinically, an imaging system would provide valuable spatial information on tissue composition. While it is feasible to build a multiplexed fiber-optic probe based spectral imaging system, these systems suffer from drawbacks with respect to cost and size. To address these I developed a compact and low cost system using a broadband light source with an 8-slot filter wheel for illumination and silicon photodiodes for detection. The spectral imaging system was tested on a set of tissue mimicking liquid phantoms which yielded an optical property extraction accuracy of 6.40 ± 7.78% for the absorption coefficient (µa) and 11.37 ± 19.62% for the wavelength-averaged reduced scattering coefficient (µs').
While DRS provided one potential approach to margin diagnosis, the technique was inherently limited in terms of lateral resolution. The second optical technique I chose to focus on was fluorescence microscopy, which had the ability to achieve lateral resolution on the order of microns. Cancer is associated with specific cellular morphological changes, such as increased nuclear size and crowding from rapidly proliferating cells. In situ tissue imaging using fluorescent stains may be useful for intraoperative detection of residual cancer in surgical tumor margins. I developed a widefield fluorescence structured illumination microscope (SIM) system with a single-shot FOV of 2.1×1.6 mm (3.4 mm2) and sub-cellular resolution (4.4 µm). The objectives of this work were to measure the relationship between illumination pattern frequency and optical sectioning strength and signal-to-noise ratio in turbid (i.e. thick) samples for selection of the optimum frequency, and to determine feasibility for detecting residual cancer on tumor resection margins, using a genetically engineered primary mouse model of sarcoma. The SIM system was tested in tissue mimicking solid phantoms with various scattering levels to determine impact of both turbidity and illumination frequency on two SIM metrics, optical section thickness and modulation depth. To demonstrate preclinical feasibility, ex vivo 50 µm frozen sections and fresh intact thick tissue samples excised from a primary mouse model of sarcoma were stained with acridine orange, which stains cell nuclei, skeletal muscle, and collagenous stroma. The cell nuclei were segmented using a high-pass filter algorithm, which allowed quantification of nuclear density. The results showed that the optimal illumination frequency was 31.7 µm−1 used in conjunction with a 4x 0.1 NA objective. This yielded an optical section thickness of 128 µm and an 8.9x contrast enhancement over uniform illumination. I successfully demonstrated the ability to resolve cell nuclei in situ achieved via SIM, which allowed segmentation of nuclei from heterogeneous tissues in the presence of considerable background fluorescence. Specifically, I demonstrated that optical sectioning of fresh intact thick tissues performed equivalently in regards to nuclear density quantification, to physical frozen sectioning and standard microscopy.
However the development of the SIM system was only the first step in showing potential application to surgical margin assessment. The nest study presented in this dissertation was to demonstrate clinical viability on a sample size of 23 animals. The biological samples used in this study were a genetically engineered mouse model of sarcoma, where a spontaneous solid tumor was grown in the hind leg. After the tumor was surgically removed from the animal and the relevant margin was stained with acridine orange (AO), a simple and widely available contrast agent that brightly stains cell nuclei and fibrous tissues. The margin was imaged with the SIM system with the primary goal of visualizing specific morphological changes in cell nuclei. To automatically segment AO-stained regions, an algorithm known as maximally stable extremal regions (MSER) was optimized and applied to the images.
As an intermediate step prior to diagnosing whole margins, a tissue-type classification model was developed to differentiate localized regions (75x75 µm) of tumor from skeletal muscle and adipose tissue based on the MSER nuclei segmentation output. A logistic regression model was used which yielded a final output in terms of probability (0-100%) the tumor within the localized region. The model performance was tested using an ROC curve analysis that revealed a 77% sensitivity and 81% specificity. For margin classification, the whole margin image was divided into localized regions and this tissue-type classification model was applied. In a subset of 6 margins (3 negative, 3 positive), it was shown that at a tumor probability threshold of 50% only 8% of all regions from a negative margins exceeded this threshold, while over 25% of all regions exceeded the threshold in the positive margins.
Item Open Access Development of Plasmonics-active Nanoconstructs for Targeting, Tracking, and Delivery in Single Cells(2010) Gregas, Molly K.Although various proof-of-concept studies have demonstrated the eventual potential of a multifunctional SERS-active metallic nanostructures for biological applications such as single cell analysis/measurement and drug delivery, the actual development and testing of such a system in vitro has remained challenging. One key point at which many potentially useful biomethods encounter difficulty lies in the translation of early proof-of-concept experiments in a clean, aqueous solution to complex, crowded, biologically-active environments such as the interior of living cells. The research hypotheses for this work state that multifunctional nanoconstructs can be fabricated and used effectively in conjunction with surface-enhanced Raman scattering (SERS) spectroscopy and other photonics-based methods to make intracellular measurements in and deliver treatment to single cells. The results of experimental work address the specific research aims, to 1) establish temporal and spatial parameters of nanoprobe uptake and modulation, 2) demonstrate targeting of functionalized nanoparticles to the cytoplasm and nucleus of single cells, 3) deliver to and activate drug treatment in cells using a multifunctional nanosystem, and 4) make intracellular measurements in normal and disease cells using external nanoprobes,
Raman spectroscopy and two-dimensional Raman imaging were used to identify and locate labeled silver nanoparticles in single cells using SERS detection. To study the efficiency of cellular uptake, silver nanoparticles were functionalized with three differently charged SERS/Raman labels and co-incubated with J774 mouse macrophage cell cultures for internalization via normal cellular processes. The surface charge on the nanoparticles was observed to modulate uptake efficiency, demonstrating a dual function of the surface modifications as tracking labels and as modulators of cell uptake.
To demonstrate delivery of functionalized nanoparticles to specific locations within the cell, silver nanoparticles were co-functionalized with the HIV-1 TAT (49-57) peptide for cell-penetrating and nuclear-targeting ability and p-mercaptobenzoic acid (pMBA) molecules as a surface-enhanced Raman scattering (SERS) label for tracking and imaging. Two-dimensional SERS mapping was used to track the spatial and temporal progress of nanoparticle uptake in PC-3 human prostate cells and to characterize localization at various time points, demonstrating the potential for an intracellularly-targeted multiplexed nanosystem. Silver nanoparticles co-functionalized with the TAT peptide showed greatly enhanced cellular uptake and nuclear localization as compared with the control nanoparticles lacking the targeting moiety.
The efficacy of targeted nanoparticles as a drug delivery vehicle was demonstrated with development and testing of an anti-cancer treatment in which novel scintillating nanoparticles functionalized with HIV-1 TAT (49-57) for cell-penetrating and nuclear-targeting ability were loaded with tethered psoralen molecules as cargo. The experiments were designed to investigate a nanodrug system consisting of psoralen tethered to a nuclear targeting peptide anchored to UVA-emitting, X-ray luminescent yttrium oxide nanoparticles. Absorption of the emitted UVA photons by nanoparticle-tethered psoralen has the potential to cross-link adenine and thymine residues in DNA located in the nucleus. Such cross-linking by free psoralen following activation with UVA light has previously been shown to cause apoptosis in vitro and an immunogenic response in vivo. Experimental results using the PC-3 human prostate cancer cell line demonstrate that X-ray excitation of these psoralen-functionalized Y2O3 nanoscintillators yields concentration-dependent reductions in cell number density when compared to control cultures containing psoralen-free Y2O3 nanoscintillators.
The development and demonstration of a small molecule-sensitive SERS-active fiber-optic nanoprobe suitable for intracellular bioanalysis was demonstrated using pH measurements in single living human cells. The proof-of-concept for the SERS-based fiber-optic nanoprobes was illustrated by measurements of intracellular pH in MCF-7 human breast cancer, HMEC-15/hTERT immortalized normal human mammary epithelial, and PC-3 human prostate cancer cells. Clinical relevance was demonstrated by pH measurements in patient biopsy cell samples. The results indicated that that fiber-optic nanoprobe insertion and interrogation provide a sensitive and selective means to monitor biologically relevant small molecules at the single cell level.
Item Open Access Dynamic Metamaterials for Far-Infrared Imaging and Spectroscopy(2019) Nadell, Christian CAs early as 1949, it was predicted that a technological gap would form in the far infrared. This so-called ``terahertz gap" is the result of two limitations. On one side, the atomic phenomena giving rise to laser technologies are difficult to extend below $10$ terahertz (THz), and on the other, microwave technologies are difficult to extend above $0.1$ THz. Even today, while this gap has closed to some extent, the generation and detection of electromagnetic radiation in this bandwidth remains inefficient and impractical, especially when compared to more mature technologies based in optical and microwave frequencies. The terahertz gap thus provides an exciting opportunity for innovation and the development of novel imaging techniques.
Metamaterials are a natural fit for the above problem because their electromagnetic properties are determined by their geometry, so they are fundamentally less limited by the physical properties of the materials of which they are composed. This means that a designed electromagnetic response can be scaled to many different bands--including the terahertz--simply by scaling the geometry accordingly. However, the process of designing and optimizing metamaterials is nontrivial and still very much an area of active research. Chapter 6 in particular will describe some new approaches for metamaterial design based on machine learning methods.
Item Embargo Electromagnetic Metamaterials for Wave Manipulation(2024) Rozman, Natalie AnnThe overarching problem addressed in this dissertation is the restricted number of devices that operate in the millimeter wave, terahertz, and infrared regimes using conventional materials. Devices designed for operation at these wavelengths are incredibly valuable across various applications such as material characterization, imaging technologies, and communication systems. However, the scarcity of devices is attributed, in part, to the limited availability of naturally occurring materials that can operate in these ranges. Therefore, there is an exciting opportunity to tailor electromagnetic metamaterials for millimeter wave, terahertz, and infrared manipulation.
Electromagnetic metamaterials have been shown to enable unique scattering effects leading to advancements in next-generation devices. One important feature of metamaterials is the ability to tune the geometry and engineer the scattered response for nearly any range of the electromagnetic spectrum. Therefore, the exploration and development of advanced electromagnetic metamaterials for use in millimeter wave, terahertz, and infrared regimes is of great importance.
Chapter 1 provides a discussion on the importance of millimeter wave, terahertz, and infrared radiation. In addition, this chapter provides an introduction to electromagnetic metamaterials. Chapters 2 and 3 discuss two metamaterials designed for operation at millimeter wavelengths. In Chapter 2, a metamaterial coherent detector is presented and in Chapter 3, a metamaterial gradient index lens is introduced.
Several metamaterials for operation in the terahertz range are studied and discussed in Chapter 4, 5, and 6. In Chapter 4, exotic physics is studied and results in the excitation of high-quality factor modes. Chapter 5 introduces an electromagnetic absorber for radiometric calibration applications. Lastly, Chapter 6 presents a metamaterial strain sensor. A reflective and transmissive metamaterial diffuser is studied in Chapter 7 for use in the infrared regime. An in-depth discussion on the fabrication of all presented metamaterials is included in Chapter 8. Finally, a summary of all presented works and concluding thoughts is included in Chapter 9.
Item Open Access Flexible Silicon Photodiode Probes for Diffuse Reflectance Spectroscopy(2016) Miller, David MichaelThe optical properties of biological tissue provide quantitative information about the physiological structure and chemical composition of a tissue sample. The investigation of tissue optical properties through Diffuse Reflectance Spectroscopy (DRS) is a rapid, non-invasive technique with extensive applications in healthcare diagnostics and therapeutics. Breast conservation surgery, a clinical practice performed for nearly 15,000 patients annually, requires accurate diagnosis of the tissue margin, the healthy layer of tissue surrounding the excised tumor. This margin assessment has traditionally been performed via post-operative pathology through one of multiple time-intensive processes that are performed after the surgery is completed. However, the margin assessment can also be rapidly performed by DRS, leading towards pathological evaluations concurrent with the excision surgery.
Presently, DRS probe designs are limited to laboratory settings. They include illumination and collection optical fibers, spectrometers, and CCD detectors, which all add to the complexity, cost, and size of a diagnostic system. Recently, DRS probes have been designed with Silicon photodetectors (Si PDs), including detector arrays that enable simultaneous DRS imaging of multiple tissue sites. The Si PDs reduce probe system complexity by replacing the cumbersome fiber-based collection probes and CCD detectors.
However, these monolithic Si PD probes are rigid and flat. When imaging non-planar tissue samples, a rigid probe may experience reduced accuracy from uneven tissue pressure and loss of contact with the tissue surface. A physically flexible DRS probe can improve sensing accuracy by conforming to a tissue surface with arbitrary curvature.
This thesis presents the design, fabrication, and test of flexible DRS Si PD probes constructed with thin film single crystalline silicon heterogeneously bonded to a flexible polymer substrate. The PDs have dark currents and responsivities comparable to high performance standard thickness Si PDs. The responsivity and zero bias dark current of the flexible PDs were evaluated while flat and while curved up to a 10 mm radius of curvature, with measured variations in responsivity (±0.61%) and dark current (±3 pA).
The flexible DRS probe was evaluated on benign and malignant breast tissue representative liquid phantoms. DRS measurements were performed with the flexible DRS probe on both liquid phantoms over a wavelength range of 470 – 600 nm at five radii of curvature: flat, 50 mm, 25 mm, 15 mm, and 10 mm. The optical contrast between the benign and malignant phantom DRS measurements ranged from 4.0-13.6% across all measured wavelengths for the flat test case and 5.9-15.5% while curved. For both phantoms at all wavelengths, the DRS signal increased in response to increasing curvature. The increase in reflectance signal ranged from 4.8-12.3% when the liquid phantom curvature was brought from flat to a 10 mm radius of curvature. The experimental results were then compared to theoretical reflectance values generated through a forward Monte Carlo model. The mean error between experiment and theory was 2.33% for the benign phantom and 1.23% for the malignant phantom.
Pixel-to-pixel crosstalk, the portion of diffusely reflected light that enters the tissue near one PD but is detected at a different PD, was also evaluated using the same test setup as for the DRS signal. The crosstalk signal also increases due to curvature, with an increase of 33.2-40.0% across all measured wavelengths for the benign phantom. The experimental crosstalk signal for the benign phantom was compared to a forward Monte Carlo model with mean error of 4.85%. The crosstalk could not be measured on the malignant phantom due to lower reflected light levels that were below the noise floor of the PD.
The flexible Si PD probe presented herein shows promising results for optical tissue analysis and feature extraction on both flat and curved tissue surfaces. This flexible probe technology facilitates conformal tissue DRS imaging, potentially in a clinical diagnostic device.
Item Open Access Insight into How the Coordination Environment of Cu Influences Chemical and Biological Activity of the Antifungal Peptide Histatin-5(2019) Conklin Lopez, StevenThe histidine-rich salivary peptides of the histatin family are known to bind copper (Cu) and other metal ions in vitro, but the details of these interactions are poorly understood and their implications on in vivo antifungal activity have not been established. Here, we explore how the coordination environment of Cu influences chemical and biological activity of the antifungal peptide Hist-5. Antifungal susceptibility assays and Cu-binding experiments reveal how the efficacy of Hist-5 against the commensal organism Candida albicans depends on the availability of Cu in the growth environment. Further, this biological activity correlates with the presence of adjacent histidine residues (bis-His) within the histatin peptide that support Cu(I) binding in the low nM range. Evaluation of oxygen reactivity of the Histatin Cu(I)-bis-His complexes indicates the PCu(I) complex is reactive towards H2O2. EPR, UV-Vis and HPLC studies demonstrate that exposure to H2O2 results in the formation of a metalloradical complex reminiscent of radical copper oxidases. Additional exploration of the coordination environment conducive to metalloradical formation exposes the importance of the third ligand (His3) of the Cu(I)-bis-His Complex for H2O2. His3 mutant peptides also disclose the tunability of the H2O2 reactivity. Furthermore, substrate evaluation assays offer evidence of the capability of the Cu-Hist-5 to specifically chemically modify a cell wall component. Together, these results provided compelling evidence supporting that Cu-coordination plays a critical role in the biological and chemical activity of Hist-5.
Item Open Access Light scattering and absorption spectroscopy in three dimensions using quantitative low coherence interferometry for biomedical applications(2011) Robles, Francisco EduardoThe behavior of light after interacting with a biological medium reveals a wealth of information that may be used to distinguish between normal and disease states. This may be achieved by simply imaging the morphology of tissues or individual cells, and/or by more sophisticated methods that quantify specific surrogate biomarkers of disease. To this end, the work presented in this dissertation demonstrates novel tools derived from low coherence interferometry (LCI) that quantitatively measure wavelength-dependent scattering and absorption properties of biological samples, with high spectral resolution and micrometer spatial resolution, to provide insight into disease states.
The presented work first describes a dual window (DW) method, which decomposes a signal sampled in a single domain (in this case the frequency domain) to a distribution that simultaneously contains information from both the original domain and the conjugate domain (here, the temporal or spatial domain). As the name suggests, the DW method utilizes two independently adjustable windows, each with different spatial and spectral properties to overcome limitations found in other processing methods that seek to obtain the same information. A theoretical treatment is provided, and the method is validated through simulations and experiments. With this tool, the spatially dependent spectral behavior of light after interacting with a biological medium may be analyzed to extract parameters of interest, such as the scattering and absorption properties.
The DW method is employed to investigate scattering properties of samples using Fourier domain LCI (fLCI). In this method, induced temporal coherence effects provide insight into structural changes in dominant scatterers, such as cell nuclei within tissue, which can reveal the early stages of cancerous development. fLCI is demonstrated in complex, three-dimensional samples using a scattering phantom and an ex-vivo animal model. The results from the latter study show that fLCI is able to detect changes in the morphology of tissues undergoing precancerous development.
The DW method is also employed to enable a novel form of optical coherence tomography (OCT), an imaging modality that uses coherence gating to obtain micrometer-scale, cross-sectional information of tissues. The novel method, named molecular imaging true color spectroscopic OCT (METRiCS OCT), analyses the depth dependent absorption of light to ascertain quantitative information of chromophore concentration, such as hemoglobin. The molecular information is also processed to yield a true color representation of the sample, a unique capability of this approach. A number of experiments, including hemoglobin absorbing phantoms and in-vivo imaging of a chick embryo model and dorsal skinfold window chamber model, demonstrate the power of the method.
The final method presented in this dissertation, consists of a spectroscopic approach that interrogates the dispersive biochemical properties of samples to independently probe the scattering and absorption coefficients. To demonstrate this method, named non-linear phase dispersion spectroscopy (NLDS), a careful analysis of LCI signals is presented. The method is verified using measurements from samples that scatter and absorb light. Lastly, NLDS is combined with phase microscopy to achieve molecular imaging with sub-micron spatial resolution. Imaging of red blood cells (RBCs) shows that the method enables highly sensitive measurements that can quantify hemoglobin content from single RBCs.
Item Open Access Melanin Chemistry Revealed by Excited State Dynamics and the Resulting Biological Implications(2014) Simpson, Mary JaneDermatopathologists need more reliable tools for analyzing biopsies of lesions that are potentially melanomas and determining the best treatment plan for the patient. Previously inaccessible, the chemical and physical properties of melanin provide insight into melanoma biochemistry. Two-color, near-infrared pump-probe microscopy of unstained, human pathology slides reveals differences in the type of melanins and the distribution of melanins between melanomas and benign nevi. Because the pump-probe response of melanin is resilient to aging, even for hundreds of millions of years, this tool could prove useful in retrospective studies to correlate melanin characteristics with patient outcome, thus eliminating the pathologist's uncertainty from the development of this classification method.
Pump-probe spectroscopy of a variety of melanin preparations including melanins with varying amounts of metal ions and toxins, those that have been photo-damaged or chemically oxidized, and melanins with a homogeneous size distribution shows that the pump-probe response is sensitive to these chemical and physical differences, not just melanin type as previously hypothesized. When sampling the response at several pump wavelengths, the specificity of this technique is derived from the absorption spectra of the underlying chromophores. Therefore, hyperspectral pump-probe microscopy of melanin could serve as an indicator of the chemical environment in a variety of biological contexts. For example, the melanin chemistry of macrophages suggests that these cells oxidize, homogenize, and compact melanin granules; whereas melanocytes produce heterogeneous melanins.
Item Embargo Modulating the Dynamics of Charged and Photoexcited-States in Nanoscale Systems(2023) Widel, Zachary Xavier WilliamLight-matter interactions are fundamental to many critical emerging technologies – such as photovoltaics, photonic sensing, and information transmission – that rely upon the efficient capture of light and its conversion to useful energetic states. However, to realize these technologies as a viable future we must first understand the fundamental processes which govern and dictate the energetic, spatial, and temporal identity of materials following photoexcitation. As is suggested by the term “light-matter” both the qualities of the light and the structural composition of the material will influence these characteristics resulting from their interaction. This dissertation investigates how photoexcitation conditions and material structure can be leveraged to modulate the energetic and charged states, and the dynamics thereof, which arise following photoexcitation of nanoscale and molecular systems. Employing ultrafast pump-probe transient absorption spectroscopy, this work characterizes the transient states which arise from photoexcitation of: (i) single-walled carbon nanotubes (SWNTs) wrapped by aryleneethynylene semiconducting polymers; (ii) covalently linked ethyne bridged porphyrin donor, rylene acceptor, molecular “ratchets” and (iii) rylene chromophores covalently linked to amino acid models. In nanoscale systems, this work highlights how the electronic structure of 1-dimensional SWNTs: (i) enable a complex interplay of excitation fluence dependent multi-body interactions, arising from the multitude of photogenerated energetic states, which may be harnessed to modulate the nature and lifetime of charge separated states and; (ii) give rise to a collection of heretofore ill-defined photoexcited-states with low energy optical transitions. At a molecular level, this work demonstrates how molecular structures can be engineered to: (i) utilize quantum coherence in a donor-acceptor “ratchet” which exhibit excitation frequency dependent uphill energy transfer, via vibronic mixing, to undergo electronically irreversible charge transfer and; (ii) selectively photooxidize amino acid analogues in biologically reminiscent photoreactions. These findings presented herein may be used to guide optoelectronic designs which efficiently guide and harness the charged and energetic species which arise from photoexcitation.
Item Open Access Photoexcited Emission Efficiencies of Zinc Oxide(2009) Foreman, John VincentOptoelectronic properties of the II-VI semiconductor zinc oxide (ZnO) have been studied scientifically for almost 60 years; however, many fundamental questions remain unanswered about its two primary emission bands--the exciton-related luminescence in the ultraviolet and the defect-related emission band centered in the green portion of the visible spectrum. The work in this dissertation was motivated by the surprising optical properties of a ZnO nanowire sample grown by the group of Prof. Jie Liu, Department of Chemistry, Duke University. We found that this nanowire sample exhibited defect-related green/white emission of unprecedented intensity relative to near-band-edge luminescence. The experimental work comprising this dissertation was designed to explain the optical properties of this ZnO nanowire sample. Understanding the physics underlying such exceptional intensity of green emission addresses many of the open questions of ZnO research and assesses the possibility of using ZnO nanostructures as an ultraviolet-excited, broadband visible phosphor.
The goal of this dissertation is to provide insight into what factors influence the radiative and nonradiative recombination efficiencies of ZnO by characterizing simultaneously the optical properties of the near-band-edge ultraviolet and the defect-related green emission bands. Specifically, we seek to understand the mechanisms of ultraviolet and green emission, the mechanism of energy transfer between them, and the evolution of their emission efficiencies with parameters such as excitation density and sample temperature. These fundamental but unanswered questions of ZnO emission are addressed here by using a novel combination of ultrafast spectroscopic techniques in conjunction with a systematic set of ZnO samples. Through this systematic investigation, ZnO may be realistically assessed as a potential green/white light phosphor.
Photoluminescence techniques are used to characterize the thermal quenching behavior of both emission bands in micrometer-scale ZnO powders. Green luminescence quenching is described by activation energies associated with bound excitons. We find that green luminescence efficiency is maximized when excitons are localized in the vicinity of green-emitting defects. Subsequent photoluminescence excitation measurements performed at multiple temperatures independently verified that green band photoluminescence intensity directly correlates with the photogenerated exciton population.
The spatial distributions of green-emitting defects and nonradiative traps are elucidated by an innovative combination of quantum efficiency and time-integrated/resolved photoluminescence measurements. By combining these techniques for the first time, we take advantage of the drastically different absorption coefficients for one- and two-photon excitations to provide details about the types and concentrations of surface and bulk defects and to demonstrate the non-negligible effects of reabsorption. A comparison of results for unannealed and annealed ZnO powders indicates that the annealing process creates a high density of green-emitting defects near the surface of the sample while simultaneously reducing the density of bulk nonradiative traps. These experimental results are discussed in the context of a simple rate equation model that accounts for the quantum efficiencies of both emission bands.
For both femtosecond pulsed and continuous-wave excitations, the green band efficiency is found to decrease with increasing excitation density--from 35% to 5% for pulsed excitation spanning 1-1000 uJ/cm2, and from 60% to 5% for continuous excitation in the range 0.01-10 W/cm2. On the other hand, near-band-edge emission efficiency increases from 0.4% to 25% for increasing pulsed excitation density and from 0.1% to 0.6% for continuous excitation. It is shown experimentally that these changes in efficiency correspond to a reduction in exciton formation efficiency. The differences in efficiencies for pulsed versus continuous-wave excitation are described by changes in the relative rates of exciton luminescence and exciton capture at green defects based on an extended rate equation model that accounts for the excitation density dependence of both luminescence bands.
In using a systematic set of ZnO samples and a novel combination of optical techniques to characterize them, this body of work presents a comprehensive and detailed physical picture of recombination mechanisms in ZnO. The insight provided by these results has immediate implications for material growth/processing techniques and should help material growers control the relative efficiencies of ultraviolet, green/visible, and nonradiative recombination channels in ZnO.
Item Open Access Quantitative Spectral Contrast in Hyperpolarized 129Xe Pulmonary MRI(2016) Robertson, Scott HaileHyperpolarized (HP) 129Xe MRI has emerged as a viable tool for evaluating lung function without ionizing radiation. HP 129Xe has already been used to image ventilation and quantify ventilation defects. However, this thesis aims to further develop imaging techniques that are capable of imaging, not just ventilation, but also gas transfer within the lung. This ability to image gas transfer directly is enabled by the solubility and chemical shifts of 129Xe that provide separate MR signatures in the airspaces, barrier tissue, and red blood cells (RBCs).
While 129Xe in the airspace (referred to as gas-phase 129Xe) can be readily imaged with standard vendor-provided imaging sequences, 129Xe in the barrier and RBC compartments (collectively referred to as dissolved-phase 129Xe) has such a rapid T2* (<2 msec at 2T) that even simple gradient recalled echo (GRE) sequences are ineffective at imaging the limited signal before it decays. To minimize these losses from T2* decay, the 3D radial sequence offers much shorter TEs that can image the dissolved-phase 129Xe. Despite their ability to image dissolved-phase signal, however, 3D radial sequences have not yet been widely adopted within the hyperpolarized gas community. In order to demonstrate the potential of the 3D radial pulse sequence, chapter 3 uses standard 129Xe ventilation imaging to compare 3D radial image quality and defect conspicuity with that of the conventional GRE. Since the 3D radial sequence offered comparable performance in ventilation imaging, and also provided the ability to image dissolved-phase 129Xe, chapter 3 establishes that the 3D radial sequence is well-suited for imaging 129Xe in humans.
Though 3D radial acquisition offers clear advantages for functional 129Xe lung imaging, its non-Cartesian sampling of k-space complicates image reconstruction. Chapter 4 carefully explains the process of gridding-based reconstruction, and describes how problems arising from non-selective RF pulses and undersampling, both of which are commonly employed in hyperpolarized 129Xe imaging, can be avoided by using appropriate reconstruction techniques. Furthermore, we detail a generalized procedure to optimize reconstruction parameters, then demonstrate the benefits of our improved reconstruction methods across both 1H anatomical imaging as well as functional imaging of 129Xe in the gas- and dissolved-phases.
These dissolved-phase images are particularly interesting because they consist of separate contributions from 129Xe in the RBCs and barrier tissue. Once these two resonances are disentangled from one another, they provide a noninvasive means to measure gas exchange regionally. However, such decomposition of these two resonances is predicated on prior knowledge of their spectroscopic properties. To that end, chapter 5 describes a non-linear spectroscopic curve fitting toolbox that we developed to more accurately characterize the 129Xe spectrum in vivo. Though previously, only two dissolved-phase resonances have ever been described within the lung, our fitting tools were able to identify a third dissolved-phase resonance in both healthy volunteers and healthy controls. Furthermore, we describe several spectroscopic features that differ statistically between our healthy volunteers and IPF subjects to demonstrate that this technique is sensitive to even subtle functional changes within the lung. These spectroscopic measurements provide the basis for imaging gas transfer.
Describing lung function regionally requires phase-sensitive imaging techniques that can decompose the dissolved-phase signal into images that represent the contribution from the RBC and barrier resonances. To date, only two implementations have been demonstrated, and both suffered from poor SNR and challenges in quantifying gas transfer. Chapter 6 adds quantitative processing techniques that improve phase sensitive imaging of 129Xe gas transfer. These methods 1) normalize both the RBC and barrier uptake images by gas-phase magnetization so that intensities can be compared across subjects, 2) compress the dynamic range of these functional images to enhance their perceived SNR, and 3) derive colormap thresholds from a healthy reference population to give intensities meaningful context.
To show the value of our quantitative gas transfer imaging, chapter 7 applies these techniques to a cohort of healthy volunteers and another of IPF patients. Since patients with IPF exhibit a progressive thickening and hardening of the pulmonary interstitium that severely restricts the transport of gases between the lungs and blood, they represent an ideal population to prove out our methods. This analysis identifies several patterns to the RBC and barrier distributions which could potentially represent different stages of disease. Furthermore, we demonstrate that our MRI-based findings correlate well with DLCO and FVC, and to a lesser extent with the structural cues seen in CT. This suggests that 129Xe imaging offers complimentary functional information that can’t be derived from CT, while also describing its spatial distribution unlike PFTs.
The work in this thesis has transitioned our HP 129Xe gas transfer studies from a proof of concept to an optimized and quantitative imaging protocol with robust processing pipelines. Using these MRI methods, we have shown that we can directly and quantitatively probe pulmonary ventilation and gas transfer within a single breath hold. In IPF, such noninvasive imaging methods are desperately needed to monitor the efficacy of these new treatments to ensure that the associated medical expense is justified with positive changes in outcomes. Finally, these new functional contrasts will be useful in studying other cardiopulmonary diseases such as asthma, chronic obstructive pulmonary disease, and pulmonary arterial hypertension.
Item Open Access Resonance-Domain Diffractive Infrared Spectrometer(2020) Deng, YangDiffractive spectroscopy has served as one of the most powerful tools in the history of physics and extends its applications to optics, astronomy, and biology. However, diffractive spectroscopy suffers from its low efficiency compared to all the newly invented spectroscopic techniques in the past century. Resonance domain designs help to improve the efficiency of existing diffractive elements. Furthermore, based on the effective grating theory, the resonance-domain diffractive lens allows both focusing and dispersion within a diffractive component.
In this thesis, the author studied the effective grating theory in the resonance domain and applied this approach to design, fabricate, and simulate a resonance-domain diffractive infrared spectrometer that operates in mid-infrared from 3µm to 5µm. The designed infrared spectrometer consists of a resonance domain diffractive lens and a single mid-infrared detector. This system achieved a stimulated efficiency of over 99%. The compact, broadband, and highly efficient spectrometer shows great promise for more extensive applications such as environmental monitoring, security screening, and biomedical research.
Item Open Access Systems and Methods for Quantitative Functional Imaging of Breast Tumor Margin Morphology(2016) Nichols, Brandon Scott\abstract
Among women, breast cancer has the highest incidence rate worldwide and remains the leading cause of cancer-related deaths in developed countries. Women with stage I or II breast cancer are eligible for a surgical procedure known as breast conserving surgery (BCS) which seeks to optimize the amount of tissue removed.BCS involves removing the tumor and a minimally thin peripheral layer, or margin of disease-free tissue surrounding the tumor. While the procedure dramatically minimizes the amount of tissue removed, an unfortunate concomitant reality is that a significant percentage (around 25$\%$) of patients will be advised to return for a second surgery due to the discovery of malignant cells at the tissue margin edge, suggesting that it is likely not all of the malignant cells were removed in the initial procedure. The fact that margins are analyzed in histopathology post-operatively (in most cases) presents a substantial clinical burden that could be reduced if the surgeon was able to reliably assess suspicious areas intra-operatively.
The primary challenge in addressing this need stems from the need to resolve microscopic cellular morphology within a relatively tremendous amount of benign breast tissue. Many investigative optical tools seek to address this challenge, as the wavelength-dependent nature of light propagation within tissue can be used to assign optical signatures to tissue types derived from the relative tissue constituents.
Among the numerous techniques, quantitative diffuse reflectance spectroscopy (QDRS) is a well-established, comparatively simple technique that has been extensively validated in simulation, tissue-simulating phantoms, and various clinical contexts to robustly provide feature-specific optical signatures related to tissue morphology. We have leveraged QDRS in an evolution of several system formats to describe the morphological state of excised breast tissue based on the endogenous optical chromophores and scatterers within the breast, specifically, the amount of hemoglobin from blood, \betac~ in fat, as well as the size distribution and number density of scatterers.
We have employed multiple hardware embodiments of this technique related to the context of use. Each device leverages the same physical principles: The diffuse reflectance spectrum is measured using an imaging probe with multiple optical channels and is analyzed with a feature extraction algorithm based on a fast, scalable \mc~ model to quantitatively determine the absorption spectrum (\mualam) and reduced scattering spectrum (\musplam). The technology detects varying amounts of malignancy in the presence of benign tissue by quantifying the margin “landscape” as a cumulative distribution function (CDF) of the ratio of \betac~ concentration (absorber) and the wavelength averaged tissue scattering (\bscat), derived from \oprop, respectively. We have established through histopathological validation that the \bscat~ reports on the relative amount of adipose to collagen, glands, and fibrous content; decreased ratios are strongly associated with the presence of residual disease.
Local recurrence in BCS has a compelling association with residual disease, suggesting that QDRS could be used to reduce re-excision rates. The work presented here demonstrates a systematic approach in the development of a pragmatic and clinically viable QDRS imaging system. Two approaches are employed: a robust, research-grade 49-channel system is used to validate previous clinical findings and determine the optimal sampling resolution, and secondly, a low-cost, portable, miniature system based on annular photodiodes is developed and shown to be diagnostically comparable. These systems are accompanied by the development of a unique imaging platform that provides robust quality control and improved resolution, further improving the diagnostic capability. The diagnostic utility of the \bscat parameter is explored in a 100-patient clinical study. The potential for commercialization of the miniature system is informed through deployment of a replica system at a remote institution. Accessibility is improved through the design of a generic, object oriented software package that abstracts the individual hardware components.
The portability, accuracy, and manufacturability provide a realistically translatable path for integration into the clinical standard of care.