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Low power, high throughput continuous flow PCR instruments for environmental applications

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Continuous monitoring in the adequate temporal and spatial scale is necessary for a better understanding of environmental variations. But field deployments of molecular biological analysis platforms in that scale are currently hindered because of issues with power, throughput and automation.

Continuous monitoring in the adequate temporal and spatial scale is necessary for a better understanding of environmental variations. But field deployments of molecular biological analysis platforms in that scale are currently hindered because of issues with power, throughput and automation. Currently, such analysis is performed by the collection of large sample volumes from over a wide area and transporting them to laboratory testing facilities, which fail to provide any real-time information. This dissertation evaluates the systems currently utilized for in-situ field analyses and the issues hampering the successful deployment of such bioanalytial instruments for environmental applications. The design and development of high throughput, low power, and autonomous Polymerase Chain Reaction (PCR) instruments, amenable for portable field operations capable of providing quantitative results is presented here as part of this dissertation. A number of novel innovations have been reported here as part of this work in microfluidic design, PCR thermocycler design, optical design and systems integration. Emulsion microfluidics in conjunction with fluorinated oils and Teflon tubing have been used for the fluidic module that reduces cross-contamination eliminating the need for disposable components or constant cleaning. A cylindrical heater has been designed with the tubing wrapped around fixed temperature zones enabling continuous operation. Fluorescence excitation and detection have been achieved by using a light emitting diode (LED) as the excitation source and a photomultiplier tube (PMT) as the detector. Real-time quantitative PCR results were obtained by using multi-channel fluorescence excitation and detection using LED, optical fibers and a 64-channel multi-anode PMT for measuring continuous real-time fluorescence. The instrument was evaluated by comparing the results obtained with those obtained from a commercial instrument and found to be comparable. To further improve the design and enhance its field portability, this dissertation also presents a framework for the instrumentation necessary for a portable digital PCR platform to achieve higher throughputs with lower power. Both systems were designed such that it can easily couple with any upstream platform capable of providing nucleic acid for analysis using standard fluidic connections. Consequently, these instruments can be used not only in environmental applications, but portable diagnostics applications as well.

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2013

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Energy efficient RF transmitter design using enhanced breakdown voltage SOI-CMOS compatible MESFETs

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The high cut-off frequency of deep sub-micron CMOS technologies has enabled the integration of radio frequency (RF) transceivers with digital circuits. However, the challenging point is the integration of RF power amplifiers, mainly due to the low breakdown voltage of

The high cut-off frequency of deep sub-micron CMOS technologies has enabled the integration of radio frequency (RF) transceivers with digital circuits. However, the challenging point is the integration of RF power amplifiers, mainly due to the low breakdown voltage of CMOS transistors. Silicon-on-insulator (SOI) metal semiconductor field effect transistors (MESFETs) have been introduced to remedy the limited headroom concern in CMOS technologies. The MESFETs presented in this thesis have been fabricated on different SOI-CMOS processes without making any change to the standard fabrication steps and offer 2-30 times higher breakdown voltage than the MOSFETs on the same process. This thesis explains the design steps of high efficiency and wideband RF transmitters using the proposed SOI-CMOS compatible MESFETs. This task involves DC and RF characterization of MESFET devices, along with providing a compact Spice model for simulation purposes. This thesis presents the design of several SOI-MESFET RF power amplifiers operating at 433, 900 and 1800 MHz with ~40% bandwidth. Measurement results show a peak power added efficiency (PAE) of 55% and a peak output power of 22.5 dBm. The RF-PAs were designed to operate in Class-AB mode to minimize the linearity degradation. Class-AB power amplifiers lead to poor power added efficiency, especially when fed with signals with high peak to average power ratio (PAPR) such as wideband code division multiple access (W-CDMA). Polar transmitters have been introduced to improve the efficiency of RF-PAs at backed-off powers. A MESFET based envelope tracking (ET) polar transmitter was designed and measured. A low drop-out voltage regulator (LDO) was used as the supply modulator of this polar transmitter. MESFETs are depletion mode devices; therefore, they can be configured in a source follower configuration to have better stability and higher bandwidth that MOSFET based LDOs. Measurement results show 350 MHz bandwidth while driving a 10 pF capacitive load. A novel polar transmitter is introduced in this thesis to alleviate some of the limitations associated with polar transmitters. The proposed architecture uses the backgate terminal of a partially depleted transistor on SOI process, which relaxes the bandwidth and efficiency requirements of the envelope amplifier in a polar transmitter. The measurement results of the proposed transmitter demonstrate more than three times PAE improvement at 6-dB backed-off output power, compared to the traditional RF transmitters.

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2012

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Codoped zinc oxide by a novel co-spray deposition technique for solar cells applications

Description

Zinc oxide (ZnO), a naturally n-type semiconductor has been identified as a promising candidate to replace indium tin oxide (ITO) as the transparent electrode in solar cells, because of its wide bandgap (3.37 eV), abundant source materials and suitable refractive

Zinc oxide (ZnO), a naturally n-type semiconductor has been identified as a promising candidate to replace indium tin oxide (ITO) as the transparent electrode in solar cells, because of its wide bandgap (3.37 eV), abundant source materials and suitable refractive index (2.0 at 600 nm). Spray deposition is a convenient and low cost technique for large area and uniform deposition of semiconductor thin films. In particular, it provides an easier way to dope the film by simply adding the dopant precursor into the starting solution. In order to reduce the resistivity of undoped ZnO, many works have been done by doping in the ZnO with either group IIIA elements or VIIA elements using spray pyrolysis. However, the resistivity is still too high to meet TCO's resistivity requirement. In the present work, a novel co-spray deposition technique is developed to bypass a fundamental limitation in the conventional spray deposition technique, i.e. the deposition of metal oxides from incompatible precursors in the starting solution. With this technique, ZnO films codoped with one cationic dopant, Al, Cr, or Fe, and an anionic dopant, F, have been successfully synthesized, in which F is incompatible with all these three cationic dopants. Two starting solutions were prepared and co-sprayed through two separate spray heads. One solution contained only the F precursor, NH 4F. The second solution contained the Zn and one cationic dopant precursors, Zn(O 2CCH 3) 2 and AlCl 3, CrCl 3, or FeCl 3. The deposition was carried out at 500 &degC; on soda-lime glass in air. Compared to singly-doped ZnO thin films, codoped ZnO samples showed better electrical properties. Besides, a minimum sheet resistance, 55.4 Ω/sq, was obtained for Al and F codoped ZnO films after vacuum annealing at 400 &degC;, which was lower than singly-doped ZnO with either Al or F. The transmittance for the Al and F codoped ZnO samples was above 90% in the visible range. This co-spray deposition technique provides a simple and cost-effective way to synthesize metal oxides from incompatible precursors with improved properties.

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2013

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Resistance switching in chalcogenide based programmable metallization cells (PMC) and sensors under gamma-rays

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Chalcogenide glass (ChG) materials have gained wide attention because of their applications in conductive bridge random access memory (CBRAM), phase change memories (PC-RAM), optical rewritable disks (CD-RW and DVD-RW), microelectromechanical systems (MEMS), microfluidics, and optical communications. One of the significant

Chalcogenide glass (ChG) materials have gained wide attention because of their applications in conductive bridge random access memory (CBRAM), phase change memories (PC-RAM), optical rewritable disks (CD-RW and DVD-RW), microelectromechanical systems (MEMS), microfluidics, and optical communications. One of the significant properties of ChG materials is the change in the resistivity of the material when a metal such as Ag or Cu is added to it by diffusion. This study demonstrates the potential radiation-sensing capabilities of two metal/chalcogenide glass device configurations. Lateral and vertical device configurations sense the radiation-induced migration of Ag+ ions in germanium selenide glasses via changes in electrical resistance between electrodes on the ChG. Before irradiation, these devices exhibit a high-resistance `OFF-state' (in the order of 10E12) but following irradiation, with either 60-Co gamma-rays or UV light, their resistance drops to a low-resistance `ON-state' (around 10E3). Lateral devices have exhibited cyclical recovery with room temperature annealing of the Ag doped ChG, which suggests potential uses in reusable radiation sensor applications. The feasibility of producing inexpensive flexible radiation sensors has been demonstrated by studying the effects of mechanical strain and temperature stress on sensors formed on flexible polymer substrate. The mechanisms of radiation-induced Ag/Ag+ transport and reactions in ChG have been modeled using a finite element device simulator, ATLAS. The essential reactions captured by the simulator are radiation-induced carrier generation, combined with reduction/oxidation for Ag species in the chalcogenide film. Metal-doped ChGs are solid electrolytes that have both ionic and electronic conductivity. The ChG based Programmable Metallization Cell (PMC) is a technology platform that offers electric field dependent resistance switching mechanisms by formation and dissolution of nano sized conductive filaments in a ChG solid electrolyte between oxidizable and inert electrodes. This study identifies silver anode agglomeration in PMC devices following large radiation dose exposure and considers device failure mechanisms via electrical and material characterization. The results demonstrate that by changing device structural parameters, silver agglomeration in PMC devices can be suppressed and reliable resistance switching may be maintained for extremely high doses ranging from 4 Mrad(GeSe) to more than 10 Mrad (ChG).

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2013

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Characterization of interface state in silicon carbide metal oxide semiconductor capacitors

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Silicon carbide (SiC) has always been considered as an excellent material for high temperature and high power devices. Since SiC is the only compound semiconductor whose native oxide is silicon dioxide (SiO2), it puts SiC in a unique position. Although

Silicon carbide (SiC) has always been considered as an excellent material for high temperature and high power devices. Since SiC is the only compound semiconductor whose native oxide is silicon dioxide (SiO2), it puts SiC in a unique position. Although SiC metal oxide semiconductor (MOS) technology has made significant progress in recent years, there are still a number of issues to be overcome before more commercial SiC devices can enter the market. The prevailing issues surrounding SiC MOSFET devices are the low channel mobility, the low quality of the oxide layer and the high interface state density at the SiC/SiO2 interface. Consequently, there is a need for research to be performed in order to have a better understanding of the factors causing the poor SiC/SiO2 interface properties. In this work, we investigated the generation lifetime in SiC materials by using the pulsed metal oxide semiconductor (MOS) capacitor method and measured the interface state density distribution at the SiC/SiO2 interface by using the conductance measurement and the high-low frequency capacitance technique. These measurement techniques have been performed on n-type and p-type SiC MOS capacitors. In the course of our investigation, we observed fast interface states at semiconductor-dielectric interfaces in SiC MOS capacitors that underwent three different interface passivation processes, such states were detected in the nitrided samples but not observed in PSG-passivated samples. This result indicate that the lack of fast states at PSG-passivated interface is one of the main reasons for higher channel mobility in PSG MOSFETs. In addition, the effect of mobile ions in the oxide on the response time of interface states has been investigated. In the last chapter we propose additional methods of investigation that can help elucidate the origin of the particular interface states, enabling a more complete understanding of the SiC/SiO2 material system.

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2015

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Distributed inference using bounded transmissions

Description

Distributed inference has applications in a wide range of fields such as source localization, target detection, environment monitoring, and healthcare. In this dissertation, distributed inference schemes which use bounded transmit power are considered. The performance of the proposed schemes are

Distributed inference has applications in a wide range of fields such as source localization, target detection, environment monitoring, and healthcare. In this dissertation, distributed inference schemes which use bounded transmit power are considered. The performance of the proposed schemes are studied for a variety of inference problems. In the first part of the dissertation, a distributed detection scheme where the sensors transmit with constant modulus signals over a Gaussian multiple access channel is considered. The deflection coefficient of the proposed scheme is shown to depend on the characteristic function of the sensing noise, and the error exponent for the system is derived using large deviation theory. Optimization of the deflection coefficient and error exponent are considered with respect to a transmission phase parameter for a variety of sensing noise distributions including impulsive ones. The proposed scheme is also favorably compared with existing amplify-and-forward (AF) and detect-and-forward (DF) schemes. The effect of fading is shown to be detrimental to the detection performance and simulations are provided to corroborate the analytical results. The second part of the dissertation studies a distributed inference scheme which uses bounded transmission functions over a Gaussian multiple access channel. The conditions on the transmission functions under which consistent estimation and reliable detection are possible is characterized. For the distributed estimation problem, an estimation scheme that uses bounded transmission functions is proved to be strongly consistent provided that the variance of the noise samples are bounded and that the transmission function is one-to-one. The proposed estimation scheme is compared with the amplify and forward technique and its robustness to impulsive sensing noise distributions is highlighted. It is also shown that bounded transmissions suffer from inconsistent estimates if the sensing noise variance goes to infinity. For the distributed detection problem, similar results are obtained by studying the deflection coefficient. Simulations corroborate our analytical results. In the third part of this dissertation, the problem of estimating the average of samples distributed at the nodes of a sensor network is considered. A distributed average consensus algorithm in which every sensor transmits with bounded peak power is proposed. In the presence of communication noise, it is shown that the nodes reach consensus asymptotically to a finite random variable whose expectation is the desired sample average of the initial observations with a variance that depends on the step size of the algorithm and the variance of the communication noise. The asymptotic performance is characterized by deriving the asymptotic covariance matrix using results from stochastic approximation theory. It is shown that using bounded transmissions results in slower convergence compared to the linear consensus algorithm based on the Laplacian heuristic. Simulations corroborate our analytical findings. Finally, a robust distributed average consensus algorithm in which every sensor performs a nonlinear processing at the receiver is proposed. It is shown that non-linearity at the receiver nodes makes the algorithm robust to a wide range of channel noise distributions including the impulsive ones. It is shown that the nodes reach consensus asymptotically and similar results are obtained as in the case of transmit non-linearity. Simulations corroborate our analytical findings and highlight the robustness of the proposed algorithm.

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2013

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Comparative analysis of simulation of trap induced threshold voltage fluctuations for 45 nm gate length n-MOSFET and analytical model predictions

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In very small electronic devices the alternate capture and emission of carriers at an individual defect site located at the interface of Si:SiO2 of a MOSFET generates discrete switching in the device conductance referred to as a random telegraph signal

In very small electronic devices the alternate capture and emission of carriers at an individual defect site located at the interface of Si:SiO2 of a MOSFET generates discrete switching in the device conductance referred to as a random telegraph signal (RTS) or random telegraph noise (RTN). In this research work, the integration of random defects positioned across the channel at the Si:SiO2 interface from source end to the drain end in the presence of different random dopant distributions are used to conduct Ensemble Monte-Carlo ( EMC ) based numerical simulation of key device performance metrics for 45 nm gate length MOSFET device. The two main performance parameters that affect RTS based reliability measurements are percentage change in threshold voltage and percentage change in drain current fluctuation in the saturation region. It has been observed as a result of the simulation that changes in both and values moderately decrease as the defect position is gradually moved from source end to the drain end of the channel. Precise analytical device physics based model needs to be developed to explain and assess the EMC simulation based higher VT fluctuations as experienced for trap positions at the source side. A new analytical model has been developed that simultaneously takes account of dopant number variations in the channel and depletion region underneath and carrier mobility fluctuations resulting from fluctuations in surface potential barriers. Comparisons of this new analytical model along with existing analytical models are shown to correlate with 3D EMC simulation based model for assessment of VT fluctuations percentage induced by a single interface trap. With scaling of devices beyond 32 nm node, halo doping at the source and drain are routinely incorporated to combat the threshold voltage roll-off that takes place with effective channel length reduction. As a final study on this regard, 3D EMC simulation method based computations of threshold voltage fluctuations have been performed for varying source and drain halo pocket length to illustrate the threshold voltage fluctuations related reliability problems that have been aggravated by trap positions near the source at the interface compared to conventional 45 nm MOSFET.

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2011

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Efficient perceptual super-resolution

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Super-Resolution (SR) techniques are widely developed to increase image resolution by fusing several Low-Resolution (LR) images of the same scene to overcome sensor hardware limitations and reduce media impairments in a cost-effective manner. When choosing a solution for the SR

Super-Resolution (SR) techniques are widely developed to increase image resolution by fusing several Low-Resolution (LR) images of the same scene to overcome sensor hardware limitations and reduce media impairments in a cost-effective manner. When choosing a solution for the SR problem, there is always a trade-off between computational efficiency and High-Resolution (HR) image quality. Existing SR approaches suffer from extremely high computational requirements due to the high number of unknowns to be estimated in the solution of the SR inverse problem. This thesis proposes efficient iterative SR techniques based on Visual Attention (VA) and perceptual modeling of the human visual system. In the first part of this thesis, an efficient ATtentive-SELective Perceptual-based (AT-SELP) SR framework is presented, where only a subset of perceptually significant active pixels is selected for processing by the SR algorithm based on a local contrast sensitivity threshold model and a proposed low complexity saliency detector. The proposed saliency detector utilizes a probability of detection rule inspired by concepts of luminance masking and visual attention. The second part of this thesis further enhances on the efficiency of selective SR approaches by presenting an ATtentive (AT) SR framework that is completely driven by VA region detectors. Additionally, different VA techniques that combine several low-level features, such as center-surround differences in intensity and orientation, patch luminance and contrast, bandpass outputs of patch luminance and contrast, and difference of Gaussians of luminance intensity are integrated and analyzed to illustrate the effectiveness of the proposed selective SR frameworks. The proposed AT-SELP SR and AT-SR frameworks proved to be flexible by integrating a Maximum A Posteriori (MAP)-based SR algorithm as well as a fast two-stage Fusion-Restoration (FR) SR estimator. By adopting the proposed selective SR frameworks, simulation results show significant reduction on average in computational complexity with comparable visual quality in terms of quantitative metrics such as PSNR, SNR or MAE gains, and subjective assessment. The third part of this thesis proposes a Perceptually Weighted (WP) SR technique that incorporates unequal weighting parameters in the cost function of iterative SR problems. The proposed approach is inspired by the unequal processing of the Human Visual System (HVS) to different local image features in an image. Simulation results show an enhanced reconstruction quality and faster convergence rates when applied to the MAP-based and FR-based SR schemes.

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2011

Ultra structurally based impedance model for oral cancer detection

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This research investigated using impedance as a minimally invasive oral cancer-screening tool by modeling healthy and diseased tissue. This research developed an ultra-structurally based tissue model for oral mucosa that is versatile enough to be easily modified to mimic the

This research investigated using impedance as a minimally invasive oral cancer-screening tool by modeling healthy and diseased tissue. This research developed an ultra-structurally based tissue model for oral mucosa that is versatile enough to be easily modified to mimic the passive electrical impedance responses of multiple benign and cancerous tissue types. This new model provides answers to biologically meaningful questions related to the impedance response of healthy and diseased tissues. This model breaks away from the old empirical top down "black box" Thèvinin equivalent model. The new tissue model developed here was created from a bottom up perspective resulting in a model that is analogous to having a "Transparent Box" where each network element relating to a specific structural component is known. This new model was developed starting with sub cellular ultra-structural components such as membranes, proteins and electrolytes. These components formed the basic network elements and topology of the organelles. The organelle networks combine to form the cell networks. The cell networks combine to make networks of cell layers and the cell layers were combined into tissue networks. This produced the complete "Transparent Box" model for normal tissue. This normal tissue model was modified for disease based on the ultra-structural pathology of each disease. The diseased tissues evaluated include cancers type one through type three; necrotic-inflammation, hyperkeratosis and the compound condition of hyperkeratosis over cancer type two. The impedance responses for each of the disease were compared side by side with the response of normal healthy tissue. Comparative evidence from the models showed the structural changes in cancer produce a unique identifiable impedance "finger print." The evaluation of the "Transparent Box" model for normal tissues and diseased tissues show clear support for using comparative impedance measurements as a clinical tool for oral cancer screening.

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2012

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Optimizing the design of partially and fully depleted MESFETs for low dropout regulators

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The constant scaling of supply voltages in state-of-the-art CMOS processes has led to severe limitations for many analog circuit applications. Some CMOS processes have addressed this issue by adding high voltage MOSFETs to their process. Although it can be a

The constant scaling of supply voltages in state-of-the-art CMOS processes has led to severe limitations for many analog circuit applications. Some CMOS processes have addressed this issue by adding high voltage MOSFETs to their process. Although it can be a completely viable solution, it usually requires a changing of the process flow or adding additional steps, which in turn, leads to an increase in fabrication costs. Si-MESFETs (silicon-metal-semiconductor-field-effect-transistors) from Arizona State University (ASU) on the other hand, have an inherent high voltage capability and can be added to any silicon-on-insulator (SOI) or silicon-on-sapphire (SOS) CMOS process free of cost. This has been proved at five different commercial foundries on technologies ranging from 0.5 to 0.15 μm. Another critical issue facing CMOS processes on insulated substrates is the scaling of the thin silicon channel. Consequently, the future direction of SOI/SOS CMOS transistors may trend away from partially depleted (PD) transistors and towards fully depleted (FD) devices. FD-CMOS are already being implemented in multiple applications due to their very low power capability. Since the FD-CMOS market only figures to grow, it is appropriate that MESFETs also be developed for these processes. The beginning of this thesis will focus on the device aspects of both PD and FD-MESFETs including their layout structure, DC and RF characteristics, and breakdown voltage. The second half will then shift the focus towards implementing both types of MESFETs in an analog circuit application. Aside from their high breakdown ability, MESFETs also feature depletion mode operation, easy to adjust but well controlled threshold voltages, and fT's up to 45 GHz. Those unique characteristics can allow certain designs that were previously difficult to implement or prohibitively expensive using conventional technologies to now be achieved. One such application which benefits is low dropout regulators (LDO). By utilizing an n-channel MESFET as the pass transistor, a LDO featuring very low dropout voltage, fast transient response, and stable operation can be achieved without an external capacitance. With the focus of this thesis being MESFET based LDOs, the device discussion will be mostly tailored towards optimally designing MESFETs for this particular application.

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2010