Two-dimensional (2-D) micro-autoradiography is typically used to identify the location of a radio-labeled ligand bound to a cellular target in tissue sections. Data, such as a histological image, combined with the autoradiographic data provide a spatial relationship of the radiolabel to cellular structures. However, the disadvantage of 2-D imaging is that it only provides a local distribution of the radiolabel within a tissue slice, and not a volumetric regional distribution in the structure of interest. The development of 3-D autoradiographic/histological visualizations would provide important information not otherwise apparent, such as the ability to visualize the distribution of the labeled agents in subcutaneous tissue. We plan to obtain digital micro-autoradiographic images and fuse them to their corresponding histological images using commercially available software. We plan to create a series of 2-D fused images. This series of 2-D fused images will then form a basis for creating 3-D visualization of autoradiographic/histological images using another commercially available software. These type of fused 3-D images, which we will refer to as micro-autoradiographic fusion tomography (MAFT), are not currently available. We will illustrate the use of MAFT with the distribution of vascular endothelial growth factor (VEGF) in subcutaneous tissue. [14C]-VEGF will be injected into rat subcutaneous tissue. VEGF has been found to stimulate angiogenesis, or the growth of new blood vessels, which could prove beneficial by aiding the function of an implantable blood glucose sensor. The diffusion coefficient for VEGF in subcutaneous tissue has not yet been characterized. MAFT would be an ideal technique to use for this type of study. My thesis will address the following specific aims: 1) To label the nicotine receptors in adult and adolescent rat brains, and to obtain digital micro-autoradiographic images and histological images; 2) To fuse a 2-D digital micro-autoradiographic image with a 2-D histological image; 3) To create a 3-D image from a series of 2-D fusion images; and 4) To assess the increased information value obtained using MAFT.

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Buildings in USA consume close to 40% of overall energy used and fenestration products (e.g. windows, doors, glazed-wall etc.) are the largest components of energy loss from buildings. Accurate evaluation of thermal performances of fenestration systems is critical in predicting the overall building energy use, and improving the product performance. Typically, two-dimensional (2-D) heat transfer analysis is used to evaluate their thermal performance as the 3-D analysis is highly complex process requiring significantly more time, effort, and cost compared to 2-D analysis. Another method of evaluation e.g. physical test in a hotbox is not possible for each product as they are too expensive. Heat transfer in fenestration products is a 3-D process and their effects on overall heat transfer need to be investigated. This thesis investigated 3-D heat transfer effects in fenestration systems in comparison to the 2-D results. No significant work has been done previously in terms of 3-D modeling of windows, which included all the three forms of heat transfer e.g. conduction, convection and radiation. Detailed 2-D and 3-D results were obtained for broad range of fenestration products in the market with a range of frame materials, spacers, insulated glass units (IGU), and sizes. All 2-D results were obtained with Therm5/Window5 (e.g. currently standard method of evaluating thermal performance) and GAMBIT/FLUENT while all 3-D results were obtained with GAMBIT/FLUENT. All the three modes of heat transfer mechanism were incorporated in the heat transfer modeling. The study showed that the overall 3-D heat transfer effects are relatively small (less than 3%) for present day framing and glazing systems. Though at individual component level (e.g. sill, head, Jamb) 3-D effects were quite significant (~10%) but they are cancelled by their opposite sign of variation when overall fenestration system effect is calculated. These 3-D heat transfer effects are higher for low conducting or more energy efficient glazing and framing systems and for smaller size products. The spacer systems did not have much impact on the 3-D effects on heat transfer. As the market transforms towards more insulating and higher performance fenestration products, 3-D effects on heat transfer would be an important factor to consider which it may require correlations to be applied to 2-D models, or may necessitate the development of dedicated 3-D fenestration heat transfer computer programs.

Micro and nanofabrication technologies have been used extensively in many biomedical and biological applications. Integration of MEMS technology and biology (BioMEMS) enables precise control of the cellular microenvironments and offers high throughput systems. The focus of this research was to develop three dimensional (3-D) isotropic microstructures for comprehensive analysis on cell-substrate interactions. The aim was to investigate whether the normal and cancerous cells differentially respond to their underlying substrate and whether the differential response of the cells leads to a novel label-free technique to distinguish between normal and cancerous cells. Three different generations of 3-D isotropic microstructures comprised of curved surfaces were developed using a single-mask, single-etch step process. Our experimental model included HS68 normal human fibroblasts, MCF10A normal human breast epithelial cells and MDA-MB-231 metastatic human breast cancer cells. Primary findings on the first generation of silicon substrates demonstrated a distinct adhesion and growth behavior in HS68 and MDA-MB-231 cells. MDA-MB-231 cells deformed while the fibroblasts stretched and elongated their cytoskeleton on the curved surfaces. Unlike fibroblasts, MDA-MB-231 cells mainly trapped and localized inside the deep microchambers. Detailed investigations on cytoskeletal organization, adhesion pattern and morphology of the cells on the second generation of the silicon substrates demonstrated that cytoskeletal prestress and microtubules organization in HS68 cells, cell-cell junction and cell-substrate adhesion strength in MCF10A cells, and deformability of MDA-MB-231 cells (obtained by using AFM technique) affect their behavior inside the etched cavities. Treatment of MDA-MB-231 cells with experimental breast cancer drug, SAHA, on the second generation of substrates, significantly altered the cells morphology, cytoarchitecture and adhesion pattern inside the 3-D microstructures. Third generation of silicon substrates was developed for comprehensive analysis on behavior of MDA-MB-231 and MCF10A cells in a co-culture system in response to SAHA drug. Formation of colonies of both cell types was evident inside the cavities within a few hours after seeding the cells on the chips. SAHA selectively altered the morphology and cytoarchitecture in MDA-MB-231 cells. Most importantly, the majority of MDA-MB-231 cells stretched inside the etched cavities, while the adhesion pattern of MCF10A cells remained unaltered. In the last part of this dissertation, using AFM analysis, we showed that the growth medium composition has a pronounced effect on cell elasticity. Our findings demonstrated that the proposed isotropic silicon microstructures have potential applications in development of biosensor platforms for cell segregation as well as conducting fundamental biological studies. / Ph. D.

Continued technology scaling together with the integration of disparate technologies in a single chip means that device performance continues to outstrip interconnect and packaging capabilities, and hence there exist many difficult engineering challenges, most notably in power management, noise isolation, and intra and inter-chip communication. Significant research effort spanning many decades has been expended on traditional VLSI integration technologies, encompassing process, circuit and architectural issues to tackle these problems. Recently however, three- dimensional (3-D) integration has emerged as a leading contender in the challenge to meet performance, heterogeneous integration, cost, and size demands through this decade and beyond. Through silicon via (TSV) based 3-D wafer-level integration is an emerging vertical interconnect methodology that is used to route the signal and power supply links through all chips in the stack vertically. Delay and signal integrity (SI) calculation for signal propagation through TSVs is a critical analysis step in the physical design of such systems. In order to reduce design time and mirror well established practices, it is desirable to carry this out in two stages, with the physical structures being modelled by parasitic parameters in equivalent circuits, and subsequent analysis of the equivalent circuits for the desired metric. This thesis addresses both these issues. Parasitic parameter extraction is carried out using a field solver to explore trends in typical technologies to gain an insight into the variation of resistive, capacitive and inductive parasitics including coupling effects. A set of novel closed-form equations are proposed for TSV parasitics in terms of physical dimensions and material properties, allowing the electrical modelling of TSV bundles without the need for computationally expensive field-solvers. Suitable equivalent circuits including capacitive and inductive coupling are derived, and comparisons with field solver provided values are used to show the accuracy of the proposed parasitic parameter models for the purpose of performance and SI analysis. The deep submicron era saw the interconnection delay rather than the gate delay become the major bottleneck in modern digital design. The nature of this problem in 3-D circuits is studied in detail in this thesis. The ubiquitous technique of repeater insertion for reducing propagation delay and signal degradation is examined for TSVs, and suitable strategies and analysis techniques are proposed. Further, a minimal power smart repeater suitable for global on-chip interconnects, which has the potential to reduce power consumption by as much as 20% with respect to a traditional inverter is proposed. A modeling and analysis methodology is also proposed, that makes the smart repeater easier to amalgamate in CAD flows at different levels of hierarchy from initial signal planning to detailed place and route when compared to alternatives proposed in the literature. Finally, the topic of system-level performance estimation for massively integrated systems is discussed. As designers are presented with an extra spatial dimension in 3-D integration, the complexity of the layout and the architectural trade-offs also increase. Therefore, to obtain a true improvement in performance, a very careful analysis using detailed models at different hierarchical levels is crucial. This thesis presents a cohesive analysis of the technological, cost, and performance trade-offs for digital and mixed-mode systems, outlining the choices available at different points in the design and their ramifications / QC 20100916

Background: Research in heart disease can be aided by modelling myocardial hemodynamics with knowledge of coronary pressure and vascular resistance measured from the geometry and morphometry of coronary vasculature. This study presents methods to automatically reconstruct accurate detailed coronary vascular anatomical models from high-resolution three-dimensional optical fluorescence cryomicrotomography image volumes for simulating blood flow in coronary arterial trees. Methods: Images of fluorescent cast and bead particles perfused into the same heart comprise the vasculature and microsphere datasets, employed in a novel combined approach to measure vasculature and simulate a flow model on the extracted coronary vascular tree for estimating regional myocardial perfusion. The microspheres are used in two capacities - as fiducial biomarker point sources for measuring the image formation in order to accurately measure the vasculature dataset and as flowing particles for measuring regional myocardial perfusion through the reconstructed vasculature. A new model-based template-matching method of vascular radius estimation is proposed that incorporates a model of the optical fluorescent image formation measured from the microspheres and a template of the vessels’ tubular geometry. Results: The new method reduced the error in vessel radius estimation from 42.9% to 0.6% in a 170 micrometer vessel as compared to the Full-Width Half Maximum method. Whole-organ porcine coronary vascular trees, automatically reconstructed with the proposed method, contained on the order of 92,000+ vessel segments in the range 0.03 – 1.9 mm radius. Discrepancy between the microsphere perfusion measurements and regional flow estimated with a 1-D steady state linear static blood flow simulation on the reconstructed vasculature was modelled with daughter-to-parent area ratio and branching angle as the parameters. Correcting the flow simulation by incorporating this model of disproportionate distribution of microspheres reduced the error from 24% to 7.4% in the estimation of fractional microsphere distribution in oblique branches with angles of 100°-120°.