Increasing the power of genome wide association studies in natural populations using repeated measures : evaluation and implementation

1. Genomewide association studies (GWAS) enable detailed dissections of the genetic basis for organisms' ability to adapt to a changing environment. In long-term studies of natural populations, individuals are often marked at one point in their life and then repeatedly recaptured. It is therefore essential that a method for GWAS includes the process of repeated sampling. In a GWAS, the effects of thousands of single-nucleotide polymorphisms (SNPs) need to be fitted and any model development is constrained by the computational requirements. A method is therefore required that can fit a highly hierarchical model and at the same time is computationally fast enough to be useful. 2. Our method fits fixed SNP effects in a linear mixed model that can include both random polygenic effects and permanent environmental effects. In this way, the model can correct for population structure and model repeated measures. The covariance structure of the linear mixed model is first estimated and subsequently used in a generalized least squares setting to fit the SNP effects. The method was evaluated in a simulation study based on observed genotypes from a long-term study of collared flycatchers in Sweden. 3. The method we present here was successful in estimating permanent environmental effects from simulated repeated measures data. Additionally, we found that especially for variable phenotypes having large variation between years, the repeated measurements model has a substantial increase in power compared to a model using average phenotypes as a response. 4. The method is available in the R package RepeatABEL. It increases the power in GWAS having repeated measures, especially for long-term studies of natural populations, and the R implementation is expected to facilitate modelling of longitudinal data for studies of both animal and human populations.

Applications of Microwave Antenna Array for Wireless Power Transmission and Radar Imaging in Complex Environment

Thesis (Ph.D.)--University of Washington, 2016-08

A New Method for Estimating the Moisture Content and Flexibility of Polymerised Bentonite Clay Mat

This paper presents a scientific development to address the current absence of a convenient technique to identify the ductile to brittle transition of bentonite clay mats. The instrumented indentation and 3-point bending tests were performed on different liquid polymer hydrated bentonite clay mats at varying moisture content. Properties measured include modified Brinell Hardness Number (BHN) and elastic structural stiffness (EI). The dependence of flexural stiffness on moisture content is demonstrated to conform to a best power function variation. The ductile to brittle transition of clay mat is affected primarily by the change in the moisture content and for the clay mat to remain flexible, critical moisture content of 1.7 times of its plastic limit is required. Results also indicate that a strong correlation between indentation hardness and the structural stiffness. The subsequent outcome in the development of a portable quality control device to monitor the acceptable moisture content level to ensure flexibility of the clay mats was also described in this paper.

Least Median Of Squares Estimation In Power Systems

Static state estimators currently in use in power systems are prone to masking by multiple bad data. This is mainly because the power system regression model contains many leverage points; typically they have a cluster pattern. As reported recently in the statistical literature, only high breakdown point estimators are robust enough to cope with gross errors corrupting such a model. This paper deals with one such estimator, the least median of squares estimator, developed by Rousseeuw in 1984. The robustness of this method is assessed while applying it to power systems. Resampling methods are developed, and simulation results for IEEE test systems discussed. © 1991 IEEE.

A semi-Lagrangian finite volume method for solving viscoelastic flow problems

Recently, there has been considerable interest in solving viscoelastic problems in 3D particularly with the improvement in modern computing power. In many applications the emphasis has been on economical algorithms which can cope with the extra complexity that the third dimension brings. Storage and computer time are of the essence. The advantage of the finite volume formulation is that a large amount of memory space is not required. Iterative methods rather than direct methods can be used to solve the resulting linear systems efficiently.

Dynamic-Data Driven Real-Time Identification for Electric Power Systems

Power system engineers face a double challenge: to operate electric power systems within narrow stability and security margins, and to maintain high reliability. There is an acute need to better understand the dynamic nature of power systems in order to be prepared for critical situations as they arise. Innovative measurement tools, such as phasor measurement units, can capture not only the slow variation of the voltages and currents but also the underlying oscillations in a power system. Such dynamic data accessibility provides us a strong motivation and a useful tool to explore dynamic-data driven applications in power systems. To fulfill this goal, this dissertation focuses on the following three areas: Developing accurate dynamic load models and updating variable parameters based on the measurement data, applying advanced nonlinear filtering concepts and technologies to real-time identification of power system models, and addressing computational issues by implementing the balanced truncation method. By obtaining more realistic system models, together with timely updated parameters and stochastic influence consideration, we can have an accurate portrait of the ongoing phenomena in an electrical power system. Hence we can further improve state estimation, stability analysis and real-time operation.

Exergetic, energetic, economic and environmental evaluation of concentrated solar power plants in Libya

The PhD project addresses the potential of using concentrating solar power (CSP) plants as a viable alternative energy producing system in Libya. Exergetic, energetic, economic and environmental analyses are carried out for a particular type of CSP plants. The study, although it aims a particular type of CSP plant – 50 MW parabolic trough-CSP plant, it is sufficiently general to be applied to other configurations. The novelty of the study, in addition to modeling and analyzing the selected configuration, lies in the use of a state-of-the-art exergetic analysis combined with the Life Cycle Assessment (LCA). The modeling and simulation of the plant is carried out in chapter three and they are conducted into two parts, namely: power cycle and solar field. The computer model developed for the analysis of the plant is based on algebraic equations describing the power cycle and the solar field. The model was solved using the Engineering Equation Solver (EES) software; and is designed to define the properties at each state point of the plant and then, sequentially, to determine energy, efficiency and irreversibility for each component. The developed model has the potential of using in the preliminary design of CSPs and, in particular, for the configuration of the solar field based on existing commercial plants. Moreover, it has the ability of analyzing the energetic, economic and environmental feasibility of using CSPs in different regions of the world, which is illustrated for the Libyan region in this study. The overall feasibility scenario is completed through an hourly analysis on an annual basis in chapter Four. This analysis allows the comparison of different systems and, eventually, a particular selection, and it includes both the economic and energetic components using the “greenius” software. The analysis also examined the impact of project financing and incentives on the cost of energy. The main technological finding of this analysis is higher performance and lower levelized cost of electricity (LCE) for Libya as compared to Southern Europe (Spain). Therefore, Libya has the potential of becoming attractive for the establishment of CSPs in its territory and, in this way, to facilitate the target of several European initiatives that aim to import electricity generated by renewable sources from North African and Middle East countries. The analysis is presented a brief review of the current cost of energy and the potential of reducing the cost from parabolic trough- CSP plant. Exergetic and environmental life cycle assessment analyses are conducted for the selected plant in chapter Five; the objectives are 1) to assess the environmental impact and cost, in terms of exergy of the life cycle of the plant; 2) to find out the points of weakness in terms of irreversibility of the process; and 3) to verify whether solar power plants can reduce environmental impact and the cost of electricity generation by comparing them with fossil fuel plants, in particular, Natural Gas Combined Cycle (NGCC) plant and oil thermal power plant. The analysis also targets a thermoeconomic analysis using the specific exergy costing (SPECO) method to evaluate the level of the cost caused by exergy destruction. The main technological findings are that the most important contribution impact lies with the solar field, which reports a value of 79%; and the materials with the vi highest impact are: steel (47%), molten salt (25%) and synthetic oil (21%). The “Human Health” damage category presents the highest impact (69%) followed by the “Resource” damage category (24%). In addition, the highest exergy demand is linked to the steel (47%); and there is a considerable exergetic demand related to the molten salt and synthetic oil with values of 25% and 19%, respectively. Finally, in the comparison with fossil fuel power plants (NGCC and Oil), the CSP plant presents the lowest environmental impact, while the worst environmental performance is reported to the oil power plant followed by NGCC plant. The solar field presents the largest value of cost rate, where the boiler is a component with the highest cost rate among the power cycle components. The thermal storage allows the CSP plants to overcome solar irradiation transients, to respond to electricity demand independent of weather conditions, and to extend electricity production beyond the availability of daylight. Numerical analysis of the thermal transient response of a thermocline storage tank is carried out for the charging phase. The system of equations describing the numerical model is solved by using time-implicit and space-backward finite differences and which encoded within the Matlab environment. The analysis presented the following findings: the predictions agree well with the experiments for the time evolution of the thermocline region, particularly for the regions away from the top-inlet. The deviations observed in the near-region of the inlet are most likely due to the high-level of turbulence in this region due to the localized level of mixing resulting; a simple analytical model to take into consideration this increased turbulence level was developed and it leads to some improvement of the predictions; this approach requires practically no additional computational effort and it relates the effective thermal diffusivity to the mean effective velocity of the fluid at each particular height of the system. Altogether the study indicates that the selected parabolic trough-CSP plant has the edge over alternative competing technologies for locations where DNI is high and where land usage is not an issue, such as the shoreline of Libya.

COMPREHENSIVE ELECTRICAL/OPTICAL/THERMAL CHARACTERIZATIONS OF HIGH POWER LIGHT EMITTING DIODES AND LASER DIODES

Thermal characterizations of high power light emitting diodes (LEDs) and laser diodes (LDs) are one of the most critical issues to achieve optimal performance such as center wavelength, spectrum, power efficiency, and reliability. Unique electrical/optical/thermal characterizations are proposed to analyze the complex thermal issues of high power LEDs and LDs. First, an advanced inverse approach, based on the transient junction temperature behavior, is proposed and implemented to quantify the resistance of the die-attach thermal interface (DTI) in high power LEDs. A hybrid analytical/numerical model is utilized to determine an approximate transient junction temperature behavior, which is governed predominantly by the resistance of the DTI. Then, an accurate value of the resistance of the DTI is determined inversely from the experimental data over the predetermined transient time domain using numerical modeling. Secondly, the effect of junction temperature on heat dissipation of high power LEDs is investigated. The theoretical aspect of junction temperature dependency of two major parameters – the forward voltage and the radiant flux – on heat dissipation is reviewed. Actual measurements of the heat dissipation over a wide range of junction temperatures are followed to quantify the effect of the parameters using commercially available LEDs. An empirical model of heat dissipation is proposed for applications in practice. Finally, a hybrid experimental/numerical method is proposed to predict the junction temperature distribution of a high power LD bar. A commercial water-cooled LD bar is used to present the proposed method. A unique experimental setup is developed and implemented to measure the average junction temperatures of the LD bar. After measuring the heat dissipation of the LD bar, the effective heat transfer coefficient of the cooling system is determined inversely. The characterized properties are used to predict the junction temperature distribution over the LD bar under high operating currents. The results are presented in conjunction with the wall-plug efficiency and the center wavelength shift.

Collimation of deuterium / 3-helium fusion products for advanced spacecraft propulsion and power

Current space exploration has transpired through the use of chemical rockets, and they have served us well, but they have their limitations. Exploration of the outer solar system, Jupiter and beyond will most likely require a new generation of propulsion system. One potential technology class to provide spacecraft propulsion and power systems involve thermonuclear fusion plasma systems. In this class it is well accepted that d-He3 fusion is the most promising of the fuel candidates for spacecraft applications as the 14.7 MeV protons carry up to 80% of the total fusion power while ‘s have energies less than 4 MeV. The other minor fusion products from secondary d-d reactions consisting of 3He, n, p, and 3H also have energies less than 4 MeV. Furthermore there are two main fusion subsets namely, Magnetic Confinement Fusion devices and Inertial Electrostatic Confinement (or IEC) Fusion devices. Magnetic Confinement Fusion devices are characterized by complex geometries and prohibitive structural mass compromising spacecraft use at this stage of exploration. While generating energy from a lightweight and reliable fusion source is important, another critical issue is harnessing this energy into usable power and/or propulsion. IEC fusion is a method of fusion plasma confinement that uses a series of biased electrodes that accelerate a uniform spherical beam of ions into a hollow cathode typically comprised of a gridded structure with high transparency. The inertia of the imploding ion beam compresses the ions at the center of the cathode increasing the density to the point where fusion occurs. Since the velocity distributions of fusion particles in an IEC are essentially isotropic and carry no net momentum, a means of redirecting the velocity of the particles is necessary to efficiently extract energy and provide power or create thrust. There are classes of advanced fuel fusion reactions where direct-energy conversion based on electrostatically-biased collector plates is impossible due to potential limits, material structure limitations, and IEC geometry. Thermal conversion systems are also inefficient for this application. A method of converting the isotropic IEC into a collimated flow of fusion products solves these issues and allows direct energy conversion. An efficient traveling wave direct energy converter has been proposed and studied by Momota , Shu and further studied by evaluated with numerical simulations by Ishikawa and others. One of the conventional methods of collimating charged particles is to surround the particle source with an applied magnetic channel. Charged particles are trapped and move along the lines of flux. By introducing expanding lines of force gradually along the magnetic channel, the velocity component perpendicular to the lines of force is transferred to the parallel one. However, efficient operation of the IEC requires a null magnetic field at the core of the device. In order to achieve this, Momota and Miley have proposed a pair of magnetic coils anti-parallel to the magnetic channel creating a null hexapole magnetic field region necessary for the IEC fusion core. Numerically, collimation of 300 eV electrons without a stabilization coil was demonstrated to approach 95% at a profile corresponding to Vsolenoid = 20.0V, Ifloating = 2.78A, Isolenoid = 4.05A while collimation of electrons with stabilization coil present was demonstrated to reach 69% at a profile corresponding to Vsolenoid = 7.0V, Istab = 1.1A, Ifloating = 1.1A, Isolenoid = 1.45A. Experimentally, collimation of electrons with stabilization coil present was demonstrated experimentally to be 35% at 100 eV and reach a peak of 39.6% at 50eV with a profile corresponding to Vsolenoid = 7.0V, Istab = 1.1A, Ifloating = 1.1A, Isolenoid = 1.45A and collimation of 300 eV electrons without a stabilization coil was demonstrated to approach 49% at a profile corresponding to Vsolenoid = 20.0V, Ifloating = 2.78A, Isolenoid = 4.05A 6.4% of the 300eV electrons’ initial velocity is directed to the collector plates. The remaining electrons are trapped by the collimator’s magnetic field. These particles oscillate around the null field region several hundred times and eventually escape to the collector plates. At a solenoid voltage profile of 7 Volts, 100 eV electrons are collimated with wall and perpendicular component losses of 31%. Increasing the electron energy beyond 100 eV increases the wall losses by 25% at 300 eV. Ultimately it was determined that a field strength deriving from 9.5 MAT/m would be required to collimate 14.7 MeV fusion protons from d-3He fueled IEC fusion core. The concept of the proton collimator has been proven to be effective to transform an isotropic source into a collimated flow of particles ripe for direct energy conversion.

A deformation model of flexible, high area-to-mass ratio debris under perturbations and validation method

A new type of space debris was recently discovered by Schildknecht in near -geosynchronous orbit (GEO). These objects were later identified as exhibiting properties associated with High Area-to-Mass ratio (HAMR) objects. According to their brightness magnitudes (light curve), high rotation rates and composition properties (albedo, amount of specular and diffuse reflection, colour, etc), it is thought that these objects are multilayer insulation (MLI). Observations have shown that this debris type is very sensitive to environmental disturbances, particularly solar radiation pressure, due to the fact that their shapes are easily deformed leading to changes in the Area-to-Mass ratio (AMR) over time. This thesis proposes a simple effective flexible model of the thin, deformable membrane with two different methods. Firstly, this debris is modelled with Finite Element Analysis (FEA) by using Bernoulli-Euler theory called “Bernoulli model”. The Bernoulli model is constructed with beam elements consisting 2 nodes and each node has six degrees of freedom (DoF). The mass of membrane is distributed in beam elements. Secondly, the debris based on multibody dynamics theory call “Multibody model” is modelled as a series of lump masses, connected through flexible joints, representing the flexibility of the membrane itself. The mass of the membrane, albeit low, is taken into account with lump masses in the joints. The dynamic equations for the masses, including the constraints defined by the connecting rigid rod, are derived using fundamental Newtonian mechanics. The physical properties of both flexible models required by the models (membrane density, reflectivity, composition, etc.), are assumed to be those of multilayer insulation. Both flexible membrane models are then propagated together with classical orbital and attitude equations of motion near GEO region to predict the orbital evolution under the perturbations of solar radiation pressure, Earth’s gravity field, luni-solar gravitational fields and self-shadowing effect. These results are then compared to two rigid body models (cannonball and flat rigid plate). In this investigation, when comparing with a rigid model, the evolutions of orbital elements of the flexible models indicate the difference of inclination and secular eccentricity evolutions, rapid irregular attitude motion and unstable cross-section area due to a deformation over time. Then, the Monte Carlo simulations by varying initial attitude dynamics and deformed angle are investigated and compared with rigid models over 100 days. As the results of the simulations, the different initial conditions provide unique orbital motions, which is significantly different in term of orbital motions of both rigid models. Furthermore, this thesis presents a methodology to determine the material dynamic properties of thin membranes and validates the deformation of the multibody model with real MLI materials. Experiments are performed in a high vacuum chamber (10-4 mbar) replicating space environment. A thin membrane is hinged at one end but free at the other. The free motion experiment, the first experiment, is a free vibration test to determine the damping coefficient and natural frequency of the thin membrane. In this test, the membrane is allowed to fall freely in the chamber with the motion tracked and captured through high velocity video frames. A Kalman filter technique is implemented in the tracking algorithm to reduce noise and increase the tracking accuracy of the oscillating motion. The forced motion experiment, the last test, is performed to determine the deformation characteristics of the object. A high power spotlight (500-2000W) is used to illuminate the MLI and the displacements are measured by means of a high resolution laser sensor. Finite Element Analysis (FEA) and multibody dynamics of the experimental setups are used for the validation of the flexible model by comparing with the experimental results of displacements and natural frequencies.

Application of the latency insertion method (LIM) to the analysis of large circuit interconnect networks

The focus of this research is to explore the applications of the finite difference formulation based on the latency insertion method (LIM) to the analysis of circuit interconnects. Special attention is devoted to addressing the issues that arise in very large networks such as on-chip signal and power distribution networks. We demonstrate that the LIM has the power and flexibility to handle various types of analysis required at different stages of circuit design. The LIM is particularly suitable for simulations of very large scale linear networks and can significantly outperform conventional circuit solvers (such as SPICE).

A three-dimensional representation method for noisy point clouds based on growing self-organizing maps accelerated on GPUs

The research described in this thesis was motivated by the need of a robust model capable of representing 3D data obtained with 3D sensors, which are inherently noisy. In addition, time constraints have to be considered as these sensors are capable of providing a 3D data stream in real time. This thesis proposed the use of Self-Organizing Maps (SOMs) as a 3D representation model. In particular, we proposed the use of the Growing Neural Gas (GNG) network, which has been successfully used for clustering, pattern recognition and topology representation of multi-dimensional data. Until now, Self-Organizing Maps have been primarily computed offline and their application in 3D data has mainly focused on free noise models, without considering time constraints. It is proposed a hardware implementation leveraging the computing power of modern GPUs, which takes advantage of a new paradigm coined as General-Purpose Computing on Graphics Processing Units (GPGPU). The proposed methods were applied to different problem and applications in the area of computer vision such as the recognition and localization of objects, visual surveillance or 3D reconstruction.

Voltage and current spectra for matrix power converters

Matrix power converters are used for transforming one alternating-current power supply to another, with different peak voltage and frequency. There are three input lines, with sinusoidally varying voltages which are 120◦ out of phase one from another, and the output is to be delivered as a similar three-phase supply. The matrix converter switches rapidly, to connect each output line in sequence to each of the input lines in an attempt to synthesize the prescribed output voltages. The switching is carried out at high frequency and it is of practical importance to know the frequency spectra of the output voltages and of the input and output currents. We determine in this paper these spectra using a new method, which has significant advantages over the prior default method (a multiple Fourier series technique), leading to a considerably more direct calculation. In particular, the determination of the input current spectrum is feasible here, whereas it would be a significantly more daunting procedure using the prior method instead.

Development of Physics-based Models and Design Optimization of Power Electronic Conversion Systems

The main objective for physics based modeling of the power converter components is to design the whole converter with respect to physical and operational constraints. Therefore, all the elements and components of the energy conversion system are modeled numerically and combined together to achieve the whole system behavioral model. Previously proposed high frequency (HF) models of power converters are based on circuit models that are only related to the parasitic inner parameters of the power devices and the connections between the components. This dissertation aims to obtain appropriate physics-based models for power conversion systems, which not only can represent the steady state behavior of the components, but also can predict their high frequency characteristics. The developed physics-based model would represent the physical device with a high level of accuracy in predicting its operating condition. The proposed physics-based model enables us to accurately develop components such as; effective EMI filters, switching algorithms and circuit topologies [7]. One of the applications of the developed modeling technique is design of new sets of topologies for high-frequency, high efficiency converters for variable speed drives. The main advantage of the modeling method, presented in this dissertation, is the practical design of an inverter for high power applications with the ability to overcome the blocking voltage limitations of available power semiconductor devices. Another advantage is selection of the best matching topology with inherent reduction of switching losses which can be utilized to improve the overall efficiency. The physics-based modeling approach, in this dissertation, makes it possible to design any power electronic conversion system to meet electromagnetic standards and design constraints. This includes physical characteristics such as; decreasing the size and weight of the package, optimized interactions with the neighboring components and higher power density. In addition, the electromagnetic behaviors and signatures can be evaluated including the study of conducted and radiated EMI interactions in addition to the design of attenuation measures and enclosures.

Leakage Temperature Dependency Aware Real-Time Scheduling for Power and Thermal Optimization

Catering to society’s demand for high performance computing, billions of transistors are now integrated on IC chips to deliver unprecedented performances. With increasing transistor density, the power consumption/density is growing exponentially. The increasing power consumption directly translates to the high chip temperature, which not only raises the packaging/cooling costs, but also degrades the performance/reliability and life span of the computing systems. Moreover, high chip temperature also greatly increases the leakage power consumption, which is becoming more and more significant with the continuous scaling of the transistor size. As the semiconductor industry continues to evolve, power and thermal challenges have become the most critical challenges in the design of new generations of computing systems. In this dissertation, we addressed the power/thermal issues from the system-level perspective. Specifically, we sought to employ real-time scheduling methods to optimize the power/thermal efficiency of the real-time computing systems, with leakage/ temperature dependency taken into consideration. In our research, we first explored the fundamental principles on how to employ dynamic voltage scaling (DVS) techniques to reduce the peak operating temperature when running a real-time application on a single core platform. We further proposed a novel real-time scheduling method, “M-Oscillations” to reduce the peak temperature when scheduling a hard real-time periodic task set. We also developed three checking methods to guarantee the feasibility of a periodic real-time schedule under peak temperature constraint. We further extended our research from single core platform to multi-core platform. We investigated the energy estimation problem on the multi-core platforms and developed a light weight and accurate method to calculate the energy consumption for a given voltage schedule on a multi-core platform. Finally, we concluded the dissertation with elaborated discussions of future extensions of our research.