This thesis presents a very efficient hybrid method for analysis and design of optical and passive photonic devices. The main focus is on unbounded wave structures. This class of photonic systems are in general very large in terms of the wavelength of the driving optical sources. The size of the problem space makes the electromagnetic modelling of these structure a very challenging problem. Our approach and main contribution has been to combine or hybridize three methods that together can handle this class of photonic structures as a whole. <br /><br /> The basis of the hybrid method is a novel Gaussian Beam Tracing method GBT. Gaussian Beams (GB) are very suitable elementary functions for tracing and tracking purposes due to their finite extent and the fact that they are good approximations for actual laser beams. The GBT presented in this thesis is based on the principle of phase matching. This method can be used to model the reflection and refraction of Gaussian beams from general curved surfaces as long as the curvature of the surface is relatively small. It can also model wave propagation in free space. The developed GBT is extremely fast as it essentially uses simple algebraic equations to find the parameters of the reflected and refracted beams once the parameters of the incident beam is known. Therefore sections of the systems whose dimensions are large relative to the optical wavelength are simulated by the GBT method. <br /><br /> Fields entering a photonic system may not possess an exact Gaussian profile. For example if an aperture limits the input laser to the system, the field is no longer a GB. In these and other similar cases the field at some aperture plane needs to be expanded into a sum of GBs. Gabor expansion has been used for this purpose. This method allows any form of field distribution on a flat or curved surface to be expanded into a sum of GBs. The resultant GBs are then launched inside the system and tracked by GBT. Calculation of the coefficients of the Gabor series is very fast (1-2 minutes on a typical computer for most applications). <br /><br /> In some cases the dimensions or physical properties of structures do not allow the application of the GBT method. For example if the curvature of a surface is very large (or its radius of curvature is very small) or if the surface contains sharp edges or sub-wavelength dimensions GBT is no longer valid. In these cases we have utilized the Finite Difference Time Domain method (FDTD). FDTD is a rigorous and very accurate full wave electromagnetic solver. The time domain form of Maxwell's equations are discretized and solved. No matrix inversion is needed for this method. If the size of the structure that needs to be analyzed is large relative to the wavelength FDTD can become increasingly time consuming. Nevertheless once a structure is simulated using FDTD for a given input, the output is expanded using Gabor expansion and the resultant beams can then be efficiently propagated through any desired system using GBT. For example if a diffraction grating is illuminated by some source, once the reflection is found using FDTD, it can be propagated very efficiently through any kind of lens or prism (or other optical structures) using GBT. Therefore the overall computational efficiency of the hybrid method is very high compared to other methods.

In the past, ray tracing has been used widely in offline rendering applications since it provided the ability to better capture high quality secondary effects such as reflection, refraction and shadows. Such effects are difficult to produce in a robust, high quality fashion with traditional, real-time rasterization algorithms. Motivated to bring the advantages to ray tracing to real-time applications, researchers have developed better and more efficient algorithms that leverage the current generation of fast, parallel CPU hardware within the past few years. This thesis provides the implementation and design details of a high performance ray tracing solution called ``RTTest'' for standard, desktop CPUs. Background information on various algorithms and acceleration structures are first discussed followed by an introduction to novel techniques used to better accelerate current, core ray tracing techniques. Techniques such as Omni-Directional Packets, Cone Proxy Traversal and Multiple Frustum Traversal are proposed and benchmarked using standard ray tracing scenes. Also, a novel soft shadowing algorithm called Edge Width Soft Shadows is proposed which achieves performance comparable to a single sampled hard shadow approach targeted at real time applications such as games. Finally, additional information on the memory layout, rendering pipeline, shader system and code level optimizations of RTTest are also discussed.

Fault diagnosis plays an important role in improving the circuit design process and the manufacturing yield. With the increasing number of gates in modern circuits, determining the source of failure in a defective circuit is becoming more and more challenging. In this research, we present an efficient effect-cause diagnosis framework for combinational VLSI circuits. The framework consists of three stages to obtain an accurate and reasonably precise diagnosis. First, an improved critical path tracing algorithm is proposed to identify an initial suspect list by backtracing from faulty primary outputs toward primary inputs. Compared to the traditional critical path tracing approach, our algorithm is faster and exact. Second, a novel probabilistic ranking model is applied to rank the suspects so that the most suspicious one will be ranked at or near the top. Several fast filtering methods are used to prune unrelated suspects. Finally, to refine the diagnosis, fault simulation is performed on the top suspect nets using several common fault models. The difference between the observed faulty behavior and the simulated behavior is used to rank each suspect. Experimental results on ISCAS85 benchmark circuits show that this diagnosis approach is efficient both in terms of memory space and CPU time and the diagnosis results are accurate and reasonably precise.

The Knife-Edge Scanning Microscope (KESM) enables imaging of an entire mouse brain at sub-micrometer resolution. By using the data sets from the KESM, we can trace the neuronal and vascular structures of the whole mouse brain. I investigated effective methods for automatic seedpoint selection on 3D data sets from the KESM. Furthermore, based on the detected seedpoints, I counted the total number of somata and traced the neuronal structures in the KESM data sets. In the first step, the acquired images from KESM were preprocessed as follows: inverting, noise filtering and contrast enhancement, merging, and stacking to create 3D volumes. Second, I used a morphological object detection algorithm to select seedpoints in the complex neuronal structures. Third, I used an interactive 3D seedpoint validation and a multi-scale approach to identify incorrectly detected somata due to the dense overlapping structures. Fourth, I counted the number of somata to investigate regional differences and morphological features of the mouse brain. Finally, I traced the neuronal structures using a local maximum intensity projection method that employs moving windows. The contributions of this work include reducing time required for setting seedpoints, decreasing the number of falsely detected somata, and improving 3D neuronal reconstruction and analysis performance.

The influence of elastic anisotropy on seismic wave propagation is often neglected for the sake of simplicity. However, ignoring anisotropy may lead to significant errors in the processing of seismic data and ultimately in a poor image of the subsurface. This is especially true in wide-aperture Vertical Seismic Profiles where waves travel both vertically and horizontally. Anisotropy has been neglected in wavefront construction methods of seismic ray-tracing until Gibson (2000), who showed they are powerful tools to simulate seismic wave propagation in three-dimensional anisotropic subsurface models. The code is currently under development using a C++ object oriented programming approach because it provides high flexibility in the design of new components and facilitates debugging and maintenance of a complex algorithm. So far, the code was used to simulate propagation in homogeneous or simple heterogeneous anisotropic velocity models mainly designed for testing purposes. In particular, it has never been applied to simulate a field dataset. We propose here an analytical method involving little algebra and that allows the design of realistic heterogeneous anisotropic models using the C++ object oriented programming approach. The new model class can model smooth multi-layered subsurface with gradients or models with many dip variations. It has been used to model first arrival times of a wide-aperture VSP dataset from the Gulf of Mexico to estimate the amount of anisotropy. The proposed velocity model is transversely isotropic. The anisotropy is constant throughout the model and is defined via Thomsen's parameters. Values in the final model are epsilon = 0.055 and delta = -0.115. The model is compatible with the a priori knowledge of the local geology and reduces the RMS average time difference between measured and computed travel times by 51% in comparison to the initial isotropic model. These values are realistic and are similar to other measurements of anisotropy in the Gulf of Mexico.

Recently, methods were developed to render various global illumination e&#64256;ects with rasterization GPUs. Among those were hardware based ray tracing and photon mapping. However, due to current GPU??s inherent architectural limitations, the e&#64259;ciency and throughput of these methods remained low. In this thesis, we propose a coherent rendering system that addresses these issues. First, we introduce new photon mapping and ray racing acceleration algorithms that facilitate data coherence and spatial locality, as well as eliminating unnecessary random memory accesses. A high level abstraction of the combined ray tracing and photon mapping streaming pipeline is introduced. Based on this abstraction, an e&#64259;cient ray tracing and photon mapping GPU is designed. Using an event driven simulator, developed for this GPU, we verify and validate the proposed algorithms and architecture. Simulation results have validated better interactive performances compared to the current GPUs.

Observing seafloor crustal deformation is often composed of acoustic ranging and GPS positioning techniques, which involves positioning of a single seabed transponder. Generally, the positional uncertainty of the seabed transponder is evaluated in terms of the slant range residuals. In order to further verify the relative positioning accuracy between seabed transponders, this study designed and fabricated a transponder lander. Three transponders were mounted on the lander to form a triangle with sides 1.505, 1.505 and 1.160 m. In addition, a data acquisition and logging system is developed to collect the lander¡¦s attitude, including pitch, roll, heading, and accelerations in three orthogonal axes. A field experiment to verify the relative positioning accuracy between seabed transponders was carried out off the coast of Kaohsiung Harbor, Taiwan. The transponder lander was deployed on the seabed at a water depth of about 300 m. Based on the attitude data collected by the logging system, the heading, pitch and roll of the transponder lander on the seabed are 123.5 degrees, 0.63 degrees and 0.62 degrees, respectively. A vessel was sailed along predetermined paths to collect observations of GPS and acoustic slant range. Then, an optimization technique combined with ray tracing method was used to estimate the positions of three transponders. The position estimates of the three transponders form a triangle with sides 1.533, 1.518 and 1.184 m, which shows that, comparing with the true values, the relative positioning error between transponders is less than 3 cm. Furthermore, based on the estimates of the transponder positions, the heading, pitch and roll of the transponder lander are calculated as 120.45 degrees, 6.43 degrees and 2.51 degrees, respectively, which are in good agreement with that measured by the attitude logging system. The experimental and evaluation results indicate that the optimization technique along with the ray tracing method is practical for precisely estimating the transponder position.

Zugl.: Koblenz, Landau (Pfalz), Univ., Diss., 2008

Thesis (M.S.)--Ohio University, November, 2009. / Title from PDF t.p. Includes bibliographical references.

Metastasis is the main cause of cancer morbidity and mortality. Despite its clinical significance, several fundamental questions about the metastatic process in humans remain unsolved. Does metastasis occur early or late in cancer progression? Do metastases emanate directly from the primary tumor or give rise to each other? How does heterogeneity in the primary tumor relate to the genetic composition of secondary lesions? Addressing these questions in representative patient populations is crucial, but has been difficult so far. Here we present a simple, scalable PCR assay that enables the tracing of tumor lineage in patient tissue specimens. Our methodology relies on somatic variation in highly mutable polyguanine (poly-G) repeats located in non-coding genomic regions. We show that poly-G mutations are present in a variety of human cancers. Using colon carcinoma as an example, we demonstrate an association between patient age at diagnosis and tumor mutational burden, suggesting that poly-G variants accumulate during normal division in colonic stem cells. We further show that poorly differentiated colon carcinomas have fewer mutations than well-differentiated tumors, possibly indicating a shorter mitotic history of the founder cell in these cancers. We collect multiple spatially separated samples from primary carcinomas and their metastases and use poly-G fingerprints to build well-supported phylogenetic trees that illuminate each patient's path of progression. Our results imply that levels of intra-tumor heterogeneity vary significantly among patients.