Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2009.Includes bibliographical references.The availability of lasers with femtosecond, ultrafast light pulses provides new opportunities and challenges in instrument design. This thesis addresses three aspects of utilizing ultrafast light pulses in two-photon excitation microscopy. First, optical fibers are routinely used in many optical instruments but their use in two-photon microscopy is very limited. As ultrafast light pulses propagate through conventional fiber optics, light pulses are dispersed and broadened, as a result of nonlinear interactions between light and material. Two-photon excitation efficiency is reduced with pulse broadening. The recent development of photonic crystal fibers allows unprecedented control of light properties through them. This thesis provides a thorough quantitative characterization of different conventional optical fibers and photonic crystal fibers enabling better utilization of these fibers for two-photon microscopic imaging. Second, two-photon microscopic imaging is relatively slow due to the sequential nature of raster scanning. Several groups have recently sought to overcome this limitation by developing a 3D-resolved wide-field two-photon microscope using the concept of temporal focusing that is based on manipulating the dispersion of ultrafast light pulses spatially. However, the existing temporal focusing systems have poor optical sectioning capability and, due to a shortage of illumination power, low actual frame rate. In this thesis, a comprehensive mathematical model is derived for temporal focusing two-photon microscope taking key instrument design parameters into account.(cont.) By optimizing instrument design and the use of high two-photon cross section quantum dots, we demonstrate single quantum dot imaging at micron level resolution at video rate. Lastly, we realize that the temporal focus concept may also be used for microfabrication. A prototype three-dimensional lithographic microfabrication system is developed and micro patterning capability based on photobleaching process is demonstrated.by Daekeun Kim.Ph.D
