<p>Speciation is a constantly ongoing process whereby reproductive isolating baririer build up over time until groups of organisms can no longer exchange genes with each other. Adaptation is thought to play a major role in the formation of these barriers, although the genetic mechanisms and geographic mode underlying the spread of barriers due to adaptive evolution is poorly understood. Critically, speciation may occur in stages through the formation of intermediate partially reproductively isolated groups. The idea of such widespread ecotypes has been the subject of great controversy over the last century. Even so, we have relatively little understanding about whether widespread ecotypes exist, wheather they are reproductively isolated, and how adaptive alleles are distributed among partially isolated groups. In this dissertation, I examined these issues in widespread coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. First, I determined that coastal and inland populations comprise distinct ecotypic groups. I then determined that these ecotypes are adapted to their respective habitats through genetically based flowering time and salt tolerance differences. I assessed the genetic architecture of these adaptations through quantitative trait loci (QTL) analysis and determined the geographic distribution of the underlying alleles through latitudinally replicated mapping populations. I quantified the contribution of these loci to adaptation in the field through the incorporation of advance generation hybrids in reciprocal transplant experiments. In the process, I discovered a widespread chromosomal inversion to be involved in the adaptive flowering time and annual/perennial life-history shift among the ecotypes. Overall, the results of this study suggest that widespread reproductively isolated ecotypes can form through the spread adaptive standing genetic variation between habitats and that chromosomal rearrangements can integral to this process.</p> / Dissertation

This research focuses on estimating the shear wave velocity (Vs) profile based on the dispersion curve obtained from SASW field test data (i.e., inversion of SASW data). It is common for the person performing the inversion to assume the prior information required to constrain the problem based on his/her own judgment. Additionally, the Vs profile is usually shown as unique without giving a range of possible solutions. For these reasons, this work focuses on: (i) studying the non-uniqueness of the solution to the inverse problem; (ii) implementing an inversion procedure that presents the estimated model parameters in a way that reflects their uncertainties; and (iii) evaluating tools that help choose the appropriate prior information. One global and one local search procedures were chosen to accomplish these purposes: a pure Monte Carlo method and the maximum likelihood method, respectively. The pure Monte Carlo method was chosen to study the non-uniqueness by looking at the range of acceptable solutions (i.e., Vs profiles) obtained with as few constraints as possible. The maximum likelihood method was chosen because it is a statistical approach, which enables us to estimate the uncertainties of the resulting model parameters and to apply tools such as the Bayesian criterion to help select the prior information objectively. The above inversion methods were implemented for synthetic data, which was produced with the same forward algorithm used during inversion. This implies that all uncertainties were caused by the nature of the SASW inversion problem (i.e., there were no uncertainties added by experimental errors in data collection, analysis of the data to create the dispersion curve, layered model to represent a real 3-D soil stratification, or wave propagation theory). At the end of the research, the maximum likelihood method of inversion and the tools for the selection of prior information were successfully used with real experimental data obtained in Memphis, Tennessee.

While shoaling from deepwater in a stratified ocean, an interfacial solitary wave (ISW) may experience waveform inversion on a continental margin. Although many oceanographers have believed that the inversion from depression to elevation may commence at the turning point where the upper and bottom layers are equal in depth, this phenomenon has not been fully verified in field observations nor in a laboratory. In this study, a series of laboratory experiments and numerical modeling were conducted on the evolution of an ISW of depression across uniform slope joining a horizontal plateau which resembles pseudo slope-shelf topography, in order to clarify this fascinating phenomenon and the variations of wave properties associated with the process. In the laboratory experiments, a depression ISW was produced by a collapse mechanism in a stratified two-layer fluid system within a steel-framed wave flume (12 m long, 0.7 m high by 0.5 m wide) at the National Sun Yat-sen University in Taiwan. The fluid density in the upper (fresh) and bottom (brine) layers was 996 and 1030 kg/m3, respectively. A series of experiments were conducted upon varying the magnitude of the most important physical factors (i.e., nominal thickness of pycnocline, depth ratio between upper and bottom layer, front gradient and shape of pseudo slope-shelf), from which the results are now discussed in four separate chapters in this thesis. Present laboratory results indicate that the process of waveform inversion took place after an ISW had experienced internal run-down, hydraulic jump, vortex motion and surge-up on the front slope, prior to its propagation onto the plateau. Moreover, the fundamental wave period of leading wave on the plateau was significantly smaller than that in the preceding sections on the front slope and the incident stage earlier, thus representing frequency downshift. Amongst the factors involved, the depth ratio between the upper and bottom layer was the most significant one for waveform inversion. Only when the upper layer was thicker than the bottom layer on the plateau of pseudo slope-shelf, waveform inversion could occur, besides the length of the plateau. On the other hand, the front gradient and shape of pseudo slope-shelf also affected the magnitude of the transmitted wave over the plateau as the wave across this specific topography. In the case of a steeper front gradient, waveform inversion became insignificant due to stronger wave reflection and intense energy dissipation caused by turbulent mixing while a depression ISW propagated over a slope-shelf; particularly against a submerged vertical cliff. As a depression ISW across pseudo slope-shelf with short plateau, intense wave breaking might occur again with vortex motion at its rear end as the newly inversed waveform reentering deep water. In this region, the upper layer was smaller than the bottom layer, hence it could not support the continuous existence of an ISW in elevation. Again, energy dissipation occurred due to turbulent mixing beyond the rear end of a short plateau. Finally, a different mode of ISW appeared within pycnocline, while its nominal thickness was larger than the amplitude of the incident wave. In addition to the laboratory investigations, numerical model was also adopted to study the variations in the flow field as an ISW propagated over a pseudo slope-shelf, in order to complement the experimental results. The results of numerical modeling revealed that the horizontal velocity in the bottom layer increased when the wave encountered the front slope, even if the depth of upper layer was thinner than that of the bottom layer on the plateau. Consequently, the velocity in the upper layer became less than that in the bottom layer when the former was thicker than that of the latter on the plateau. On the other hand, the vertical velocity within the self-generated vortex switched direction as waveform inversion commenced after the wave across the shoulder of pseudo slope-shelf where the local depth of the upper layer was larger than that of bottom part. Overall, the significance of the four pertinent factors (i.e., nominal thickness of pycnocline, water depth ratio, front slope, and plateau length) that affected a depression ISW across pseudo slope-shelf is discussed in detail in this thesis, as well as the variation of flow field calculated by the numerical mode presented.

Recently, with advances in CMOS process, the RF receiver which is integrated into the SOC chip can effectively reduce production costs. When designing the wireless receiver, one of the most important technologies is to design channel-selection filter. Typically, the design of the channel-selection filter in multi-standard high-frequency will take up a large chip area and higher power consumption. Therefore, in order to reduce the area and power consumption, this thesis designed a low-power OTA and low-pass filter. This thesis presents a multi-mode wireless communication application in the receiver channel selection filter. This filter is designed to use the fifth-order Butterworth low pass filter, the filter range can be used in Bluetooth, cdma2000, wideband CDMA, and IEEE 802.11a/b/g/n wireless LAN. Using floating transistor architecture in the input stage of OTA can effectively increase the THD performance. Using MOS transistors operating in triode region and combined with current multiplier can achieve the voltage-to-current conversion. Using the trans-linear loop can reach a wide tunable range, and the OTA operating in weak inversion region can significantly reduce the transconductance. Implementation is to use the TSMC 0.18£gm CMOS process. Simulation results show that the successful operation of this filter can be between 650 kHz ~ 22MHz frequency range. The filter may have compatibility in different wireless communication applications. 14.5mW to 17.5mW, respectively, is the smallest to the largest power consumption. The supply voltage is 1.2 volts.

In this thesis, we propose a high density non-classical unipolar CMOS width two embedded oxide (2EO) NMOS load. The words ¡§unipolar CMOS¡¨ refer to the fact that the conventional NMOS driver and the proposed 2EO NMOS load are presented in which the electron is the only carrier used. Among them, the 2EO scheme is used to isolate the inversion current. And the dominant current in the 2EO NMOS load is the punch through current which is not a destructive current mechanism. Our proposed CMOS, due to the same carrier used, does not have to compensate the layout width in load design. In addition, the shared terminal of output contacts and the elimination of N-well technique are also presented in our proposed CMOS. Therefore, the layout area can be reduced 72%, in comparison with conventional CMOS. Furthermore, the packing density can be increased and the fabrication cost can be reduced, respectively. We also find out that the delay time can be improved 39% to increase the operating frequency, as compared with the convention CMOS.

Thermoacoustic tomography (TAT) is a newly emerging modality in biomedical imaging. It combines the good contrast of electromagnetic and good resolution of ultrasound imaging. The mathematical model of TAT is the observability problem for the wave equation: one observes the data on a hyper-surface and reconstructs the initial perturbation. In this dissertation, we consider several mathematical problems of TAT. The first problem is the inversion formulas. We provide a family of closed form inversion formulas to reconstruct the initial perturbation from the observed data. The second problem is the range description. We present the range description of the spherical mean Radon transform, which is an important transform in TAT. The next problem is the stability analysis for TAT. We prove that the reconstruction of the initial perturbation from observed data is not H¨older stable if some observability condition is violated. The last problem is the speed determination. The question is whether the observed data uniquely determines the ultrasound speed and initial perturbation. We provide some initial results on this issue. They include the unique determination of the unknown constant speed, a weak local uniqueness, a characterization of the non-uniqueness, and a characterization of the kernel of the linearized operator.

Horizontal well temperature and pressure distributions can be measured by production logging or downhole permanent sensors, such as fiber optic distributed temperature sensors (DTS). Correct interpretation of temperature and pressure data can be used to obtain downhole flow conditions, which is key information to control and optimize horizontal well production. However, the fluid flow in the reservoir is often multiphase and complex, which makes temperature and pressure interpretation very difficult. In addition, the continuous measurement provides transient temperature behavior which increases the complexity of the problem. To interpret these measured data correctly, a comprehensive model is required. In this study, an interpretation model is developed to predict flow profile of a horizontal well from downhole temperature and pressure measurement. The model consists of a wellbore model and a reservoir model. The reservoir model can handle transient, multiphase flow and it includes a flow model and a thermal model. The calculation of the reservoir flow model is based on the streamline simulation and the calculation of reservoir thermal model is based on the finite difference method. The reservoir thermal model includes thermal expansion and viscous dissipation heating which can reflect small temperature changes caused by pressure difference. We combine the reservoir model with a horizontal well flow and temperature model as the forward model. Based on this forward model, by making the forward calculated temperature and pressure match the observed data, we can inverse temperature and pressure data to downhole flow rate profiles. Two commonly used inversion methods, Levenberg- Marquardt method and Marcov chain Monte Carlo method, are discussed in the study. Field applications illustrate the feasibility of using this model to interpret the field measured data and assist production optimization. The reservoir model also reveals the relationship between temperature behavior and reservoir permeability characteristic. The measured temperature information can help us to characterize a reservoir when the reservoir modeling is done only with limited information. The transient temperature information can be used in horizontal well optimization by controlling the flow rate until favorite temperature distribution is achieved. With temperature feedback and inflow control valves (ICVs), we developed a procedure of using DTS data to optimize horizontal well performance. The synthetic examples show that this method is useful at a certain level of temperature resolution and data noise.

Pore type variations account for complex velocity-porosity relationship and intensive permeability heterogeneity and consequently low oil and gas recovery in carbonate reservoir. However, it is a challenge for geologist and geophysicist to quantitatively estimate the influences of pore type complexity on velocity variation at a given porosity and porosity-permeability relationship. A new rock physics-based integrated approach in this study was proposed to quantitatively characterize the diversity of pore types and its influences on wave propagation in carbonate reservoir. Based on above knowledge, permeability prediction accuracy from petrophysical data can be improved compared to conventional approach. Two carbonate reservoirs with different reservoir features, one is a shallow carbonate reservoir with average high porosity (>10%) and another one is a supper-deep carbonate reservoir with average low porosity (<5%), are used to test the proposed approach. Paleokarst is a major event to complicate carbonate reservoir pore structure. Because of limited data and lack of appropriate study methods, it is a difficulty to characterize subsurface paleokarst 3D distribution and estimate its influences on reservoir heterogeneity. A method by integrated seismic characterization is applied to delineate a complex subsurface paleokarst system in the Upper San Andres Formation, Permian basin, West Texas. Meanwhile, the complex paleokarst system is explained by using a carbonate platform hydrological model, similar to modern marine hydrological environments within carbonate islands. How to evaluate carbonate reservoir permeability heterogeneity from 3D seismic data has been a dream for reservoir geoscientists, which is a key factor to optimize reservoir development strategy and enhance reservoir recovery. A two-step seismic inversions approach by integrating angle-stack seismic data and rock physics model is proposed to characterize pore-types complexity and further to identify the relative high permeability gas-bearing zones in low porosity reservoir (< 5%) using ChangXing super-deep carbonate reservoir as an example. Compared to the conventional permeability calculation method by best-fit function between porosity and permeability, the results in this study demonstrate that gas zones and non-gas zones in low porosity reservoir can be differentiated by using above integrated permeability characterization method.

The North Anatolian Fault (NAF) is one of the world&rsquo / s largest active continental strikeslip faults, and forms the northern margin of the Anatolian plate. Although its geologic and geomorphologic features are well defined, crustal deformation and associated seismicity around central segment of the NAF is relatively less-known. In this study, we analyzed locations and focal mechanisms of 172 events with magnitude &ge / 3, which are recorded by 39 broadband seismic stations deployed by the North Anatolian Passive Seismic Experiment (2005-2008). Distribution of the events shows that the local seismicity in the area is widely distributed, suggesting a widespread continental deformation, particularly in the southern block. For the entire data set, P- and S- arrival times are picked and events are relocated using the HYPOCENTER program. Then, relocated events which have a good azimuthal coverage with a maximum gap of 120&deg / and at least 13 P- wave readings are selected and 1-D inversion algorithm, VELEST, is used to derive the 1-D seismic velocity model of the region. The final model with updated locations is later put together to the FOCMEC program, to obtain focal mechanisms solutions. In this step, an iterative scheme is applied by increasing the number of data errors. To obtain more unique solutions, first motions of P and SH v phases are used along with SH/P amplitude ratios. Resultant 109 well-constrained focal mechanisms later used to perform stress tensor inversion across the region. Our focal mechanisms suggest a dominant strike-slip deformation along two major fault sets in the region. In the east, E-W trending splays (Ezinepazari, Almus, and La&ccedil / in Kizilirmak) show right-lateral strike-slip motion similar to the NAF whereas in the west, N-S trending faults (Dodurga, Eldivan) show left lateral strike-slip motion. Overall, stress orientations are found as: maximum principal stress, &sigma / 1, is found to be subhorizontal striking NW-SE, the intermediate principle stress, &sigma / 2, is vertically orientated and the minimum principal stress, &sigma / 3, is found to be NE &ndash / SW striking, consistent with the strike-slip regime of the region.

Tsunami forecasting methodology developed by the United States National Oceanic and Atmospheric Administration&rsquo / s Center for Tsunami Research is based on the concept of a pre-computed tsunami database which includes tsunami model results from Mw 7.5 earthquakes called tsunami source functions. Tsunami source functions are placed along the subduction zones of the oceans of the world in several rows. Linearity of tsunami propagation in an open ocean allows scaling and/or combination of the pre-computed tsunami source functions. An offshore scenario is obtained through inverting scaled and/or combined tsunami source functions against Deep-ocean Assessment and Reporting of Tsunami (DART) buoy measurements. A graphical user interface called Genetic Algorithm for INversion (GAIN) was developed in MATLAB using general optimization toolbox to perform an inversion. The 15 November 2006 Kuril and 27 February 2010 Chile tsunamis are chosen as case studies. One and/or several DART buoy measurement(s) is/are used to test different error minimization functions with/without earthquake magnitude as constraint. The inversion results are discussed comparing the forecasting model results with the tide gage measurements.