Abstract: Nonlinear multicontrast microscopy is established in this study as an important tool for understanding biological structure and function of muscle cells. Second harmonic generation, third harmonic generation and multi-photon excitation fluorescence are acquired simultaneously in order to establish the origin of nonlinear signal generation in myocytes, and investigate myocyte structure and functionality during muscle contraction. Using structural cross-correlation image analysis, an algorithm developed specifically for this research, for the first time, third harmonic generation is shown to originate from the mitochondria in myocytes. The second harmonic, which is generated from the anisotropic bands of the sarcomeres, is further shown to be dependent on the crystalline order of the sarcomeres, thereby providing a potential diagnostic tool to evaluate disorder in muscle cells. The combination of the second and third harmonic provides complementary information that can be used to further elucidate the basic principles of muscle contraction. Time-lapse nonlinear microscopic imaging showed structural and functional dynamics in the myocytes. The second harmonic contrast revealed nonsynchronized nanocontractions of sarcomeres in relaxed, non-contracting, cardiomyocytes and Drosophila muscle samples, providing insight into the asynchronous behaviour of individual sarcomeres. Furthermore, macrocontracting samples were found to exhibit a synchronization of nanocontractions, providing new evidence for how muscles contract. Dynamic image correlation analysis, another algorithm developed specifically for this investigation, is used to reveal networks of mitochondria, which show fluctuations of multi-photon excitation fluorescence and third harmonic generation signals. The intensity fluctuations in the networks reveal both slow and fast dynamics; phase shifts of the slow dynamics between different networks are observed. Fast dynamics appear only in the inner networks, suggesting functional difference between interfibrillar and subsarcolemma mitochondria. The groundwork for studying bioenergetics of mitochondria in cardiomyocytes with nonlinear multimodal microscopy is fully developed in this work. The origin of the nonlinear signals and the development of the image analysis techniques provide a solid foundation to further study of muscle contractility and bioenergetics.

Genetic algorithm is often used to find the global optimum in a multi-dimensional search problem. Inspired by the natural evolution process, this algorithm employs three reproduction strategies -- cloning, crossover and mutation -- combined with selection, to improve the population as the evolution progresses from generation to generation. Femtosecond laser pulse tailoring, with the use of a pulse shaper, has become an important technology which enables applications in femtochemistry, micromachining and surgery, nonlinear microscopy, and telecommunications. Since a particular pulse shape corresponds to a point in a highly-dimensional parameter space, genetic algorithm is a popular technique for optimal pulse shape control in femtosecond laser experiments. We use genetic algorithm to optimize third harmonic generation (THG), and investigate various pulse shaper options. We test our setup by running the experiment with varied initial conditions and study factors that affect convergence of the algorithm to the optimal pulse shape. Our next step is to use the same setup to control coherent anti-Stocks Raman scattering. The results show that the THG signal has been enhanced.

Collagen is an important structural protein in living organisms and plays an indispensable role in connecting cells and tissues, such as in musculature, bone, and ligament. The stability and conformation of collagen are, however, strongly influenced by ambient temperature and constitutes an interesting subject of study. Thermally induced conformation change of collagen has been investigated by techniques such as differential scanning calorimetry (DSC) and second harmonic generation. DSC is a powerful method in uncovered important thermal dynamics properties including phase change, enthalpy, and thermal stability of the collagen. However, due to its collective nature, no localized information can be found. For comparison, second harmonic generation, which reflects structural symmetry, can be combined with laser scanning microscopy to investigate localized variation. It has been shown in previous studies that the thermal stability of collagen is strongly influenced by the water content within collagen. For comparison, we are investigating the conformational change of collagen under a vacuum stat with second harmonic microscopy so as to isolate environmental effects, particularly those from water and oxygen. In this way, we have found the conformational change of collagen takes place at a much higher temperature and activation energy. Additionally, the high spatial resolution achieved also allows many further possibilities.

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Thesis (Ph. D.)--University of Texas at Austin, 2000. / Vita. Includes bibliographical references (leaves 72-82). Available also in a digital version from Dissertation Abstracts.

Thesis (Ph. D.)--University of Chicago, Department of Chemistry, 2002. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph.D)--Physics, Georgia Institute of Technology, 2010. / Committee Chair: Rick Trebino; Committee Member: Ahmet Erbil; Committee Member: John Buck; Committee Member: Stephen Ralph; Committee Member: Zhigang Jiang. Part of the SMARTech Electronic Thesis and Dissertation Collection.

Nonlinear microscopy has become an indispensable tool in the study of biological systems. It includes many nonlinear contrast mechanisms, each sensitive to different biological structures. However, interpretation of the images generated in nonlinear microscopy is a complex matter due to factors such as the structural complexity of the sample, phase relationships between the excitation beam and the detected signal and the nonlinear interactions in the focal volume of the microscope. This thesis contains a new theoretical and numerical framework that describes the focusing of an excitation beam in a nonlinear microscope, the nonlinear optical interactions with the material in the focal volume, and the resulting nonlinear optical signal in the far field. The framework is the first to include reflection and refraction of the excitation beam and nonlinear signals by an arbitrary number of interfaces in the focal volume, which is especially significant for the interpretation of third harmonic generation (THG). It also uses the chirp-z transform to speed up calculations by orders of magnitude compared to numerical integration techniques. The framework is used to investigate second harmonic generation (SHG) by collagen. Focusing effects alter polarization-dependent SHG measurements of collagen properties compared to the plane wave approximation, and this is verified experimentally. Furthermore, a technique of imaging the far field SHG radiation from collagen fibres is proposed, which can be used to extract the orientation of collagen fibres unambiguously. The framework is then applied to analyze the influence of interfaces on THG. Reflection effects at interfaces significantly affect THG, which leads to the development of a new super-resolution THG imaging technique based on backward-propagating THG. This super-resolution technique is experimentally demonstrated by imaging surface profiles with tens of nanometers resolution, which is the first time that such resolution is obtained in coherent nonlinear microscopy. Therefore, this imaging technique shows promise to become an important tool in high-resolution imaging of (biological) samples. The theoretical and numerical framework provides a foundation for future research on the origin of nonlinear microscopy signals. The new imaging techniques based on this framework have great potential in quantifying fibrillar structures and interfaces in biological samples.

Nonlinear microscopy has become an indispensable tool in the study of biological systems. It includes many nonlinear contrast mechanisms, each sensitive to different biological structures. However, interpretation of the images generated in nonlinear microscopy is a complex matter due to factors such as the structural complexity of the sample, phase relationships between the excitation beam and the detected signal and the nonlinear interactions in the focal volume of the microscope. This thesis contains a new theoretical and numerical framework that describes the focusing of an excitation beam in a nonlinear microscope, the nonlinear optical interactions with the material in the focal volume, and the resulting nonlinear optical signal in the far field. The framework is the first to include reflection and refraction of the excitation beam and nonlinear signals by an arbitrary number of interfaces in the focal volume, which is especially significant for the interpretation of third harmonic generation (THG). It also uses the chirp-z transform to speed up calculations by orders of magnitude compared to numerical integration techniques. The framework is used to investigate second harmonic generation (SHG) by collagen. Focusing effects alter polarization-dependent SHG measurements of collagen properties compared to the plane wave approximation, and this is verified experimentally. Furthermore, a technique of imaging the far field SHG radiation from collagen fibres is proposed, which can be used to extract the orientation of collagen fibres unambiguously. The framework is then applied to analyze the influence of interfaces on THG. Reflection effects at interfaces significantly affect THG, which leads to the development of a new super-resolution THG imaging technique based on backward-propagating THG. This super-resolution technique is experimentally demonstrated by imaging surface profiles with tens of nanometers resolution, which is the first time that such resolution is obtained in coherent nonlinear microscopy. Therefore, this imaging technique shows promise to become an important tool in high-resolution imaging of (biological) samples. The theoretical and numerical framework provides a foundation for future research on the origin of nonlinear microscopy signals. The new imaging techniques based on this framework have great potential in quantifying fibrillar structures and interfaces in biological samples.

Optical imaging has been developed quickly in the past decades because it has become an important research tool in biology, biochemistry, and biomedical sciences. Coherence domain optical imaging is one of the well developed optical imaging modalities, as it provides high resolution and long penetration depth. In this dissertation, we will report our work on development of molecular contrast in coherence domain optical imaging. In order to image important molecules which are poor fluorophores, we developed a high resolution molecular imaging technique, pump-probe optical coherence microscopy (PPOCM), which does not rely on fluorescent tags. PPOCM is the fusion of Pump-Probe spectroscopy and optical coherence microscopy (OCM). We have demonstrated the prototype system on a fixed human skin sample containing a nodular melanoma. The results indicate that PPOCM can clearly provide strong contrast between the melanotic and amelanotic regions. This technique can be applied to early diagnosis of melanoma and the mapping of tumor margins during excision. It also can be extended to any biological chromophore with a known absorption spectrum and sufficient concentration. In order to differentiate further multiple chromophores, we developed a spectrally resolved two color pump-probe Optical Coherence Microscopy (SRPPOCM). We showed the prototype system on a red hair and a black hair. Our preliminary results show that the SRPPOCM technique could provide a contrast between pheomelanin and eumelanin. This technique could be used potentially as a clinical tool for diagnosing different progression stages of melanoma. This technique could also be applied to differentiate other mixed chromophores. Second harmonic optical coherence tomography (SHOCT) is non-linear high resolution optical molecular imaging modality which is widely used in non-centrosymmetric material. However, depth ambiguity is associated with SHOCT in tissue sample because forward generated second harmonic signal does not correctly report where the second harmonic signal is generated. We studied the feasibility of collecting the backward generated second harmonic signal from nanocrystals through a Second Harmonic Optical Coherence Tomography in Fourier domain. The preliminary result shows that we can collect backward generated second harmonic signal from nanocrystals which indicates that this technique could suppress the depth ambiguity.