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- Title
- Design and Implementation of Silicon-Based MEMS Resonators for Application in Ultra Stable High Frequency Oscillators.
- Creator
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Shahraini, Sarah, Abdolvand, Reza, Gong, Xun, Sundaram, Kalpathy, Kapoor, Vikram, Rajaraman, Swaminathan, University of Central Florida
- Abstract / Description
-
The focus of this work is to design and implement resonators for ultra-stable high-frequency ((>)100MHz) silicon-based MEMS oscillators. Specifically, two novel types of resonators are introduced that push the performance of silicon-based MEMS resonators to new limits. Thin film Piezoelectric-on-Silicon (TPoS) resonators have been shown to be suitable for oscillator applications due to their combined high quality factor, coupling efficiency, power handling and doping-dependent temperature...
Show moreThe focus of this work is to design and implement resonators for ultra-stable high-frequency ((>)100MHz) silicon-based MEMS oscillators. Specifically, two novel types of resonators are introduced that push the performance of silicon-based MEMS resonators to new limits. Thin film Piezoelectric-on-Silicon (TPoS) resonators have been shown to be suitable for oscillator applications due to their combined high quality factor, coupling efficiency, power handling and doping-dependent temperature-frequency behavior. This thesis is an attempt to utilize the TPoS platform and optimize it for extremely stable high-frequency oscillator applications.To achieve the said objective, two main research venues are explored. Firstly, quality factor is systematically studied and anisotropy of single crystalline silicon (SCS) is exploited to enable high-quality factor side-supported radial-mode (aka breathing mode) TPoS disc resonators through minimization of anchor-loss. It is then experimentally demonstrated that in TPoS disc resonators with tethers aligned to [100], unloaded quality factor improves from ~450 for the second harmonic mode at 43 MHz to ~11,500 for the eighth harmonic mode at 196 MHz. Secondly, thickness quasi-Lam(&)#233; modes are studied and demonstrated in TPoS resonators for the first time. It is shown that thickness quasi-Lam(&)#233; modes (TQLM) could be efficiently excited in silicon with very high quality factor (Q). A quality factor of 23.2 k is measured in vacuum at 185 MHz for a fundamental TQLM-TPoS resonators designed within a circular acoustic isolation frame. Quality factor of 12.6 k and 6 k are also measured for the second- and third- harmonic TQLM TPoS resonators at 366 MHz and 555 MHz respectively. Turn-over temperatures between 40 (&)deg;C to 125 (&)deg;C are also designed and measured for TQLM TPoS resonators fabricated on degenerately N-doped silicon substrates. The reported extremely high quality factor, very low motional resistance, and tunable turn-over temperatures (>)80 (&)#186;C make these resonators a great candidate for ultra-stable oven-controlled high-frequency MEMS oscillators.
Show less - Date Issued
- 2019
- Identifier
- CFE0007861, ucf:52775
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0007861
- Title
- Integration of High-Q filters with Highly Efficient Antennas.
- Creator
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Yusuf, Yazid, Gong, Xun, Wahid, Parveen, Jones, W, Wu, Xinzhang, Wang, Jing, University of Central Florida
- Abstract / Description
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The integration of high-quality (Q)-factor 3-D filters with highly efficient antennas is addressed in this dissertation. Integration of filters and antennas into inseparable units eliminates the transitions between the otherwise separate structures resulting in more compact and efficient systems. The compact, highly efficient integrated 3-D filter/antenna systems, enabled by the techniques developed herein, allow for the realization of integrated RF front ends with significantly- reduced form...
Show moreThe integration of high-quality (Q)-factor 3-D filters with highly efficient antennas is addressed in this dissertation. Integration of filters and antennas into inseparable units eliminates the transitions between the otherwise separate structures resulting in more compact and efficient systems. The compact, highly efficient integrated 3-D filter/antenna systems, enabled by the techniques developed herein, allow for the realization of integrated RF front ends with significantly- reduced form factors.Integration of cavity filters with slot antennas in a single planar substrate is first demonstrated. Due to the high Q factor of cavity resonators, the efficiency of the integrated filter/antenna system is found to be the same as that of a reference filter with the same filtering characteristics. This means a near 100% efficient slot antenna is achieved within this integrated filter/antenna system. To further reduce the footprint of the integrated systems, vertically integrated filter/antenna systems are developed. We then demonstrate the integration of cavity filters with aperture antenna structures which enable larger bandwidths compared with slot antennas. The enhanced bandwidths are made possible through the excitation and radiation of surface waves. To obtain omnidirectional radiation patterns , we integrate cavity filters with monopole antennas. Finally, the integration of filters with patch antennas is addressed. Unlike the other filter/antenna integration examples presented, in which the antenna is utilized as an equivalent load, the patch antenna provides an additional pole in the filtering function.The presented techniques in this dissertation can be applied for filter/antenna integration in all microwave, and millimeter-wave frequency regions.
Show less - Date Issued
- 2011
- Identifier
- CFE0004183, ucf:49075
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004183
- Title
- RIGOROUS ANALYSIS OF WAVE GUIDING AND DIFFRACTIVE INTEGRATED OPTICAL STRUCTURES.
- Creator
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Greenwell, Andrew, Moharam, M.G., University of Central Florida
- Abstract / Description
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The realization of wavelength scale and sub-wavelength scale fabrication of integrated optical devices has led to a concurrent need for computational design tools that can accurately model electromagnetic phenomena on these length scales. This dissertation describes the physical, analytical, numerical, and software developments utilized for practical implementation of two particular frequency domain design tools: the modal method for multilayer waveguides and one-dimensional lamellar gratings...
Show moreThe realization of wavelength scale and sub-wavelength scale fabrication of integrated optical devices has led to a concurrent need for computational design tools that can accurately model electromagnetic phenomena on these length scales. This dissertation describes the physical, analytical, numerical, and software developments utilized for practical implementation of two particular frequency domain design tools: the modal method for multilayer waveguides and one-dimensional lamellar gratings and the Rigorous Coupled Wave Analysis (RCWA) for 1D, 2D, and 3D periodic optical structures and integrated optical devices. These design tools, including some novel numerical and programming extensions developed during the course of this work, were then applied to investigate the design of a few unique integrated waveguide and grating structures and the associated physical phenomena exploited by those structures. The properties and design of a multilayer, multimode waveguide-grating, guided mode resonance (GMR) filter are investigated. The multilayer, multimode GMR filters studied consist of alternating high and low refractive index layers of various thicknesses with a binary grating etched into the top layer. The separation of spectral wavelength resonances supported by a multimode GMR structure with fixed grating parameters is shown to be controllable from coarse to fine through the use of tightly controlled, but realizable, choices for multiple layer thicknesses in a two material waveguide; effectively performing the simultaneous engineering of the wavelength dispersion for multiple waveguide grating modes. This idea of simultaneous dispersion band tailoring is then used to design a multilayer, multimode GMR filter that possesses broadened angular acceptance for multiple wavelengths incident at a single angle of incidence. The effect of a steady-state linear loss or gain on the wavelength response of a GMR filter is studied. A linear loss added to the primary guiding layer of a GMR filter is shown to produce enhanced resonant absorption of light by the GMR structure. Similarly, linear gain added to the guiding layer is shown to produce enhanced resonant reflection and transmission from a GMR structure with decreased spectral line width. A combination of 2D and 3D modeling is utilized to investigate the properties of an embedded waveguide grating structure used in filtering/reflecting an incident guided mode. For the embedded waveguide grating, 2D modeling suggests the possibility of using low index periodic inclusions to create an embedded grating resonant filter, but the results of 3D RCWA modeling suggest that transverse low index periodic inclusions produce a resonant lossy cavity as opposed to a resonant reflecting mirror. A novel concept for an all-dielectric unidirectional dual grating output coupler is proposed and rigorously analyzed. A multilayer, single-mode, high and graded-index, slab waveguide is placed atop a slightly lower index substrate. The properties of the individual gratings etched into the waveguide's cover/air and substrate/air interfaces are then chosen such that no propagating diffracted orders are present in the device superstrate and only a single order is present outside the structure in the substrate. The concept produces a robust output coupler that requires neither phase-matching of the two gratings nor any resonances in the structure, and is very tolerant to potential errors in fabrication. Up to 96% coupling efficiency from the substrate-side grating is obtained over a wide range of grating properties.
Show less - Date Issued
- 2007
- Identifier
- CFE0001635, ucf:47244
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0001635
- Title
- TWO-DIMENSIONAL GUIDED MODE RESONANT STRUCTURES FOR SPECTRAL FILTERING APPLICATIONS.
- Creator
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Boonruang, Sakoolkan, Moharam, M. G., University of Central Florida
- Abstract / Description
-
Guided mode resonant (GMR) structures are optical devices that consist of a planar waveguide with a periodic structure either imbedded in or on the surface of the structure. The resonance anomaly in GMR structures has many applications as dielectric mirrors, tunable devices, sensors,and narrow spectral band reflection filters. A desirable response from a resonant grating filter normally includes a nearly 100% narrowband resonant spectral reflection (transmission), and a broad angular...
Show moreGuided mode resonant (GMR) structures are optical devices that consist of a planar waveguide with a periodic structure either imbedded in or on the surface of the structure. The resonance anomaly in GMR structures has many applications as dielectric mirrors, tunable devices, sensors,and narrow spectral band reflection filters. A desirable response from a resonant grating filter normally includes a nearly 100% narrowband resonant spectral reflection (transmission), and a broad angular acceptance at either normal incidence or an oblique angle of incidence. This dissertation is a detailed study of the unique nature of the resonance anomaly in GMR structures with two-dimensional (2-D) periodic perturbation. Clear understanding of the resonance phenomenon is developed and novel 2-D GMR structures are proposed to significantly improve the performance of narrow spectral filters. In 2-D grating diffraction, each diffracted order inherently propagates in its distinct diffraction plane. This allows for coupled polarization dependent resonant leaky modes with one in each diffraction plane. The nature of the interaction between these non-collinear guides and its impact on spectral and angular response of GMR devices is investigated and quantified for 2-D structures with rectangular and hexagonal grids. Based on the developed understanding of the underlying phenomenon, novel GMR devices are proposed and analyzed. A novel controllable multi-line guided mode resonant (GMR) filter is proposed. The separation of spectral wavelength resonances supported by a two-dimensional GMR structure can be coarse or fine depending on the physical dimensions of the structure and not the material properties. Multiple resonances are produced by weakly guided modes individually propagating along multiple planes of diffraction. Controllable two-line and three-line narrow-band reflection filter designs with spectral separation from a few up to hundreds of nanometers are exhibited using rectangular-lattice and hexagonal-lattice grating GMR structures, respectively. Broadening of the angular response of narrow band two-dimension guided mode resonant spectral filters, while maintaining a narrow spectral response, is investigated. The angular response is broadened by coupling the diffracted orders into multiple fundamental guided resonant modes. These guided modes have the same propagation constant but propagating in different planes inherent in multiple planes of diffraction of the 2-D gratings. The propagation constants of the guided resonant modes are determined from the physical dimensions of the grating (periodicity and duty cycle) and the incident direction. A five-fold improvement in the angular tolerance is achieved using a grating with strong second Bragg diffraction in order to produce a crossed diffraction. A novel dual grating structure with a second grating located on the substrate side is proposed to further broaden the angular tolerance of the spectral filter without degrading its spectral response. This strong second Bragg backward diffraction from the substrate grating causes two successive resonant bands to merge producing a resonance with symmetric broad angular response.
Show less - Date Issued
- 2007
- Identifier
- CFE0001825, ucf:47346
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0001825
- Title
- FINE-SCALE STRUCTURES IN SATURN'S RINGS:WAVES, WAKES AND GHOSTS.
- Creator
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BAILLIE, Kevin, Colwell, Joshua, University of Central Florida
- Abstract / Description
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The Cassini mission provided wonderful tools to explore Saturn, its satellites and its rings system. The UVIS instrument allowed stellar occultation observations of structures in the rings with the best resolution available (around 10 meters depending on geometry and navigation), bringing our understanding of the physics of the rings to the next level. In particular, we have been able to observe, dissect, model and test the interactions between the satellites and the rings. We first looked at...
Show moreThe Cassini mission provided wonderful tools to explore Saturn, its satellites and its rings system. The UVIS instrument allowed stellar occultation observations of structures in the rings with the best resolution available (around 10 meters depending on geometry and navigation), bringing our understanding of the physics of the rings to the next level. In particular, we have been able to observe, dissect, model and test the interactions between the satellites and the rings. We first looked at kilometer-wide structures generated by resonances with satellites orbiting outside the main rings. The observation of structures in the C ring and their association with a few new resonances allowed us to estimate some constraints on the physical characteristics of the rings. However, most of our observed structures could not be explained with simple resonances with external satellites and some other mechanism has to be involved. We located four density waves associated with the Mimas 4:1, the Atlas 2:1, the Mimas 6:2 and the Pandora 4:2 Inner Lindblad Resonances and one bending wave excited by the Titan -1:0 Inner Vertical Resonance. We could estimate a range of surface mass density from 0.22 +/- 0.03 to 1.42 +/- 0.21 gcm^-2 and mass extinction coefficient from 0.13 +/- 0.03 to 0.28 +/- 0.06 cm^2 g^-1. These mass extinction coefficient values are higher than those found in the A ring (0.01 - 0.02 cm^2 g^-1) and in the Cassini Division (0.07 - 0.12 cm^2 g^-1 from Colwell et al. (2009), implying smaller particle sizes in the C ring. We can therefore imagine that the particles composing these different rings have either different origins or that their size distributions are not primordial and have evolved differently. We also estimate the mass of the C ring to be between 3.7 +/- 0.9 x 10^16 kg and 7.9 +/- 2.0 x 10^16 kg, equivalent to a moon of 28.0 +/- 2.3 km to 36.2 +/- 3.0 km radius (a little larger than Pan or Atlas) with a density comparable to the two moons (400 kg m^-3). From the wave damping length and the ring viscosity, we also estimate the vertical thickness of the C ring to be between 1.9 +/- 0.4 m and 5.6 +/- 1.4 m, which is consistent with the vertical thickness of the Cassini Division (2 - 20 m) from Tiscareno et al. (2007) and Colwell et al. (2009). Conducting similar analysis in the A, B rings and in the Cassini Division, we were able to estimate consistent masses with previous works for the these rings. We then investigated possible interactions between the rings and potential embedded satellites. Looking for satellite footprints, we estimated the possibility that some observed features in the Huygens Ringlet could be wakes of an embedded moon in the Huygens gap. We discredited the idea that these structures could actually be satellite wakes by estimating the possible position of such a satellite. Finally, we observed a whole population of narrow and clear holes in the C ring and the Cassini Division. Modeling these holes as depletion zones opened by the interaction of a moonlet inside the disk material (this signature is called a "propeller"), we could estimate a distribution of the meter-sized to house-sized objects in these rings. Similar objects, though an order of magnitude larger, have been visually identified in the A ring. In the C ring, we have signatures of boulders which sizes are estimated between 1.5 and 14.5 m, whereas similar measures in the Cassini Division provide moonlet sizes between 0.36 and 58.1 m. Using numerical simulations for the propeller formation, we estimate that our observed moonlets belong to a population of bigger particles than the one we thought was composing the rings: Zebker et al. (1985) described the ring particles population as following a power-law size distribution with cumulative index around 1.75 in the Cassini Division and 2.1 in the C ring. We believe propeller boulders follow a power-law with a cumulative index of 0.6 in the C ring and 0.8 in the Cassini Division. The question of whether these boulders are young, ephemeral and accreted inside the Roche limit or long-lived and maybe formed outisde by fragmentation of a larger body before migrating inward in the disk, remains a mystery. Accretion and fragmentation process are not yet well constrained and we can hope that Cassini extended mission will still provide a lot of information about it.
Show less - Date Issued
- 2011
- Identifier
- CFE0003947, ucf:48681
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003947
- Title
- Homologous Pairing Through DNA Driven Harmonics - A Simulation Investigation.
- Creator
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Calloway, Richard, Proctor, Michael, Kincaid, John, Jaganathan, Balasubramanian, Gerber, Matthew, Chai, Xinqing, University of Central Florida
- Abstract / Description
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The objective of this research is to determine if a better understanding of the (")molecule of life("), deoxyribonucleic acid or DNA can be obtained through Molecular Dynamics (MD) modeling and simulation (M(&)S) using contemporary MD M(&)S. It is difficult to overstate the significance of the DNA molecule. The now-completed Human Genome Project stands out as the most significant testimony yet to the importance of understanding DNA. The Human Genome Project (HGP) enumerated many areas of...
Show moreThe objective of this research is to determine if a better understanding of the (")molecule of life("), deoxyribonucleic acid or DNA can be obtained through Molecular Dynamics (MD) modeling and simulation (M(&)S) using contemporary MD M(&)S. It is difficult to overstate the significance of the DNA molecule. The now-completed Human Genome Project stands out as the most significant testimony yet to the importance of understanding DNA. The Human Genome Project (HGP) enumerated many areas of application of genomic research including molecular medicine, energy sources, environmental applications, agriculture and livestock breeding to name just a few. (Science, 2008) In addition to the fact that DNA contains the informational blueprints for all life, it also exhibits other remarkable characteristics most of which are either poorly understood or remain complete mysteries. One of those completely mysterious characteristics is the ability of DNA molecules to spontaneously segregate with other DNA molecules of similar sequence. This ability has been observed for years in living organisms and is known as (")homologous pairing.(") It is completely reproducible in a laboratory and defies explanation. What is the underlying mechanism that facilitates long-range attraction between 2 double-helix DNA molecules containing similar nucleotide sequences? The fact that we cannot answer this question indicates we are missing a fundamental piece of information concerning the DNA bio-molecule. The research proposed herein investigated using the Nano-scale Molecular Dynamics NAMD (Phillips et al., 2005) simulator the following hypotheses:H(Simulate Observed Closure NULL) : = Current MD force field models when used to model DNA molecule segments, contain sufficient variable terms and parameters to describe and reproduce directed segregating movement (closure of the segments) as previously observed by the Imperial College team between two Phi X 174 DNA molecules. H(Resonance NULL) : = Current MD force field models when used to model DNA molecule segments in a condensed phased solvent contain sufficient variable terms and parameters to reproduce theorized molecular resonation in the form of frequency content found in water between the segments. H(Harmonized Resonance NULL) : = Current MD force field models of DNA molecule segments in a condensed phase solvent produce theorized molecular resonation in the form of frequency content above and beyond the expected normal frequency levels found in water between the segments. H(Sequence Relationship NULL): = The specific frequencies and amplitudes of the harmonized resonance postulated in H(Harmonized Resonance NULL) are a direct function of DNA nucleotide sequence. H(Resonance Causes Closure NULL) : = Interacting harmonized resonation produces an aggregate force between the 2 macro-molecule segments resulting in simulation of the same directed motion and segment closure as observed by the Imperial College team between two Phi X 174 DNA molecules. After nearly six months of molecular dynamic simulation for H(Simulate Observed Closure NULL) and H(Resonance Causes Closure NULL) no evidence of closure between two similar sequenced DNA segments was found. There exist several contributing factors that potentially affected this result that are described in detail in the Results section. Simulations investigating H( Resonance NULL), H(Harmonized Resonance NULL) and the emergent hypothesis H(Sequence Relationship NULL) on the other hand, revealed a rich selection of periodic pressure variation occurring in the solvent between simulated DNA molecules. About 20% of the power in Fourier coefficients returned by Fast Fourier Transforms performed on the pressure data was characterized as statistically significant and was located in less than 2% of the coefficients by count. This unexpected result occurred consistently in 5 different system configurations with considerable system-to-system variation in both frequency and magnitude. After careful analysis given the extent of our experiments the data was found to be in support of H( Resonance NULL), and H(Harmonized Resonance NULL) . Regarding the emergent hypothesis H(Sequence Relationship NULL), further analysis was done on the aggregate data set looking for correlation between nucleotide sequence and frequency/magnitude. Some of the results may be related to sequence but were insufficient to prove it. Overall the conflicting results were inconclusive so the hypothesis was neither accepted nor rejected. Of particular interest to future researchers it was noted that the computational simulations performed herein were NOT able to reproduce what we know actually happens in a laboratory environment. DNA segregation known to occur in-vitro during the Imperial College investigation did not occur in our simulation. Until this discrepancy is resolved MM simulation should not as yet be considered a suitable tool for further investigation of Homologous Chromosome Pairing. In Chapter 5 specific follow on research is described in priority of need addressing several new questions.
Show less - Date Issued
- 2011
- Identifier
- CFE0004472, ucf:49302
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004472
- Title
- PLASMON ENHANCED NEAR-FIELD INTERACTIONS IN SURFACE COUPLED NANOPARTICLE ARRAYS FOR INTEGRATED NANOPHOTONIC DEVICES.
- Creator
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Ghoshal, Amitabh, Kik, Pieter, University of Central Florida
- Abstract / Description
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The current thrust towards developing silicon compatible integrated nanophotonic devices is driven by need to overcome critical challenges in electronic circuit technology related to information bandwidth and thermal management. Surface plasmon nanophotonics represents a hybrid technology at the interface of optics and electronics that could address several of the existing challenges. Surface plasmons are electronic charge density waves that can occur at a metal-dielectric interface at...
Show moreThe current thrust towards developing silicon compatible integrated nanophotonic devices is driven by need to overcome critical challenges in electronic circuit technology related to information bandwidth and thermal management. Surface plasmon nanophotonics represents a hybrid technology at the interface of optics and electronics that could address several of the existing challenges. Surface plasmons are electronic charge density waves that can occur at a metal-dielectric interface at optical and infrared frequencies. Numerous plasmon based integrated optical devices such as waveguides, splitters, resonators and multimode interference devices have been developed, however no standard integrated device for coupling light into nanoscale optical circuits exists. In this thesis we experimentally and theoretically investigate the excitation of propagating surface plasmons via resonant metal nanoparticle arrays placed in close proximity to a metal surface. It is shown that this approach can lead to compact plasmon excitation devices. Full-field electromagnetic simulations of the optical illumination of metal nanoparticle arrays near a metal film reveal the presence of individual nanoparticle resonances and collective grating-like resonances related to propagating surface plasmons within the periodic array structure. Strong near-field coupling between the nanoparticle and grating resonances is observed, and is successfully described by a coupled oscillator model. Numerical simulations of the effect of nanoparticle size and shape on the excitation and dissipation of surface plasmons reveal that the optimum particle volume for efficient surface plasmon excitation depends sensitively on the particle shape. This observation is quantitatively explained in terms of the shape-dependent optical cross-section of the nanoparticles. Reflection measurements on nanoparticle arrays fabricated using electron-beam lithography confirm the predicted particle-grating interaction. An unexpected polarization-dependent splitting of the film-mediated collective resonance is successfully attributed to the existence of out-of plane polarization modes of the metal nanoparticles. In order to distinguish between the excitation of propagating surface plasmons and localized nanoparticle plasmons, spectrally resolved leakage radiation measurements are presented. Based on these measurements, a universally applicable method for measuring the wavelength dependent efficiency of coupling free-space radiation into guided surface plasmon modes on thin films is developed. Finally, it is shown that the resonantly enhanced near-field coupling the nanoparticles and the propagating surface plasmons can lead to optimized coupler device dimensions well below 10 microns.
Show less - Date Issued
- 2010
- Identifier
- CFE0003091, ucf:48322
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003091
- Title
- WIRELESSLY SENSING RESONATE FREQUENCY OF PASSIVE RESONATORS WITH DIFFERENT Q VALUES.
- Creator
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Lukacs, Mathew, Gong, Xun, University of Central Florida
- Abstract / Description
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Numerous techniques exist for measuring temperature using passive devices such as SAW filters. However, SAW filters have a significant limitation regarding high temperature environments exceeding 1000C. There are several applications for a high temperature sensor in this range, most notably heat flux or temperature in turbine engines. For these environments, an alternative to SAW filters is to use a passive resonator. The resonate frequency will vary depending on the environment temperature....
Show moreNumerous techniques exist for measuring temperature using passive devices such as SAW filters. However, SAW filters have a significant limitation regarding high temperature environments exceeding 1000C. There are several applications for a high temperature sensor in this range, most notably heat flux or temperature in turbine engines. For these environments, an alternative to SAW filters is to use a passive resonator. The resonate frequency will vary depending on the environment temperature. Understanding how the frequency changes with temperature will allow us to determine the environmental temperature. In order for this approach to work, it is necessary to induce resonance in the device and measure the resonance frequency. However, the extreme high temperature makes wired connections impractical, therefore wireless interrogation is necessary. To be practical a system of wireless interrogation of up to 20cm is desired.
Show less - Date Issued
- 2011
- Identifier
- CFE0003709, ucf:48828
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003709
- Title
- Wearable Passive Wireless MEMS Respiration Sensor.
- Creator
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Moradian, Sina, Abdolvand, Reza, Sundaram, Kalpathy, Kapoor, Vikram, University of Central Florida
- Abstract / Description
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In this study a passive sensor that wirelessly monitors the profile of the human respiratory system is presented. The sensor was designed to be wearable, weighs less than 10 grams and is durable. The sensor is made of a RF piezoelectric MEMS resonator and an ultra-high frequency antenna made of a thin metal film formed on a flexible substrate . The resonance frequency of the TPoS resonator shifts as a function of condensation and evaporation of water vapor on the surface of the resonator and...
Show moreIn this study a passive sensor that wirelessly monitors the profile of the human respiratory system is presented. The sensor was designed to be wearable, weighs less than 10 grams and is durable. The sensor is made of a RF piezoelectric MEMS resonator and an ultra-high frequency antenna made of a thin metal film formed on a flexible substrate . The resonance frequency of the TPoS resonator shifts as a function of condensation and evaporation of water vapor on the surface of the resonator and changes in resonator's temperature. These parameters change in each in response to inspiration and expiration and a wireless measurement system detects the frequency shift of the sensor and converts it into the respiration profile. The respiration profile of a healthy human subject is measured and presented for a transmitter to sensor to receiver distance of ~25cm.
Show less - Date Issued
- 2017
- Identifier
- CFE0006628, ucf:51279
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006628
- Title
- The cytopathic activity of cholera toxin requires a threshold quantity of cytosolic toxin.
- Creator
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Bader, Carly, Teter, Kenneth, Zervos, Antonis, Jewett, Travis, Tatulian, Suren, University of Central Florida
- Abstract / Description
-
Cholera toxin (CT), secreted from Vibrio cholerae, causes a massive fluid and electrolyte efflux in the small intestine that results in life-threatening diarrhea and dehydration which impacts 3-5 million people per year. CT is secreted into the intestinal lumen but acts within the cytosol of intestinal epithelial cells. CT is an AB5 toxin that has a catalytic A1 subunit and a cell binding B subunit. CT moves from the cell surface to the endoplasmic reticulum (ER) by retrograde transport. Much...
Show moreCholera toxin (CT), secreted from Vibrio cholerae, causes a massive fluid and electrolyte efflux in the small intestine that results in life-threatening diarrhea and dehydration which impacts 3-5 million people per year. CT is secreted into the intestinal lumen but acts within the cytosol of intestinal epithelial cells. CT is an AB5 toxin that has a catalytic A1 subunit and a cell binding B subunit. CT moves from the cell surface to the endoplasmic reticulum (ER) by retrograde transport. Much of the toxin is transported to the lysosomes for degradation, but a secondary pool of toxin is diverted to the Golgi apparatus and then to the ER. Here the A1 subunit detaches from the rest of the toxin and enters the cytosol. The disordered conformation of free CTA1 facilitates toxin export to the cytosol by activating a quality control mechanism known as ER-associated degradation. The return to a folded structure in the cytosol allows CTA1 to attain an active conformation for modification of its Gs? target through ADP-ribosylation. This modification locks the protein in an active state which stimulates adenylate cyclase and leads to elevated levels of cAMP. A chloride channel located in the apical enterocyte membrane opens in response to signaling events induced by these elevated cAMP levels. The osmotic movement of water into the intestinal lumen that results from the chloride efflux produces the characteristic profuse watery diarrhea that is seen in intoxicated individuals.The current model of intoxication proposes only one molecule of cytosolic toxin is required to affect host cells, making therapeutic treatment nearly impossible. However, based on emerging evidence, we hypothesize a threshold quantity of toxin must be present within the cytosol of the target cell in order to elicit a cytopathic effect. Using the method of surface plasmon resonance along with toxicity assays, I have, for the first time, directly measured the efficiency of toxin delivery to the cytosol and correlated the levels of cytosolic toxin to toxin activity. I have shown CTA1 delivery from the cell surface to the cytosol is an inefficient process with only 2.3 % of the surface bound CTA1 appearing in the cytosol after 2 hours of intoxication. I have also determined and a cytosolic quantity of more than approximately .05ng of cytosolic CTA1 must be reached in order to elicit a cytopathic effect. Furthermore, CTA1 must be continually delivered from the cell surface to the cytosol in order to overcome the constant proteasome-mediated clearance of cytosolic toxin. When toxin delivery to the cytosol was blocked, this allowed the host cell to de-activate Gs?, lower cAMP levels, and recover from intoxication. Our work thus indicates it is possible to treat cholera even after the onset of disease. These findings challenge the idea of irreversible cellular toxicity and open the possibility of post-intoxication treatment options.
Show less - Date Issued
- 2013
- Identifier
- CFE0004810, ucf:49759
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004810
- Title
- Performance optimization of lateral-mode thin-film piezoelectric-on-substrate resonant systems.
- Creator
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Fatemi, Hedy, Abdolvand, Reza, Sundaram, Kalpathy, Malocha, Donald, Gong, Xun, Cho, Hyoung Jin, University of Central Florida
- Abstract / Description
-
The main focus of this dissertation is to characterize and improve the performance of thin-film piezoelectric-on-substrate (TPoS) lateral-mode resonators and filters. TPoS is a class of piezoelectric MEMS devices which benefits from the high coupling coefficient of the piezoelectric transduction mechanism while taking advantage of superior acoustic properties of a substrate. The use of lateral-mode TPoS designs allows for fabrication of dispersed-frequency filters on a single substrate, thus...
Show moreThe main focus of this dissertation is to characterize and improve the performance of thin-film piezoelectric-on-substrate (TPoS) lateral-mode resonators and filters. TPoS is a class of piezoelectric MEMS devices which benefits from the high coupling coefficient of the piezoelectric transduction mechanism while taking advantage of superior acoustic properties of a substrate. The use of lateral-mode TPoS designs allows for fabrication of dispersed-frequency filters on a single substrate, thus significantly reducing the size and manufacturing cost of devices. TPoS filters also offer a lower temperature coefficient of frequency, and better power handling capability compared to rival technologies all in a very small footprint.Design and fabrication process of the TPoS devices is discussed. Both silicon and diamond substrates are utilized for fabrication of TPoS devices and results are compared. Specifically, the superior acoustic properties of nanocrystalline diamond in scaling the frequency and energy density of the resonators is highlighted in comparison with silicon. The performance of TPoS devices in a variety of applications is reported. These applications include lateral-mode TPoS filters with record low IL values (as low as 2dB) and fractional bandwidth up to 1%, impedance transformers, very low phase noise oscillators, and passive wireless temperature sensors.
Show less - Date Issued
- 2015
- Identifier
- CFE0005945, ucf:50805
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0005945
- Title
- SOFT SWITCHING MULTI-RESONANT FORWARD CONVERTER DC TO DC APPLICATION FOR COMMUNICATIONS EQUIPMENT.
- Creator
-
Bills, David, Batarseh, Issa, University of Central Florida
- Abstract / Description
-
In the field of power electronics there is always a push to create smaller and more efficient power conversion systems. This push is driven by the industry that uses the power systems, and can be realized by new semiconductor devices or new techniques. This examination describes a novel technique for a small and highly efficient method of converting relatively high DC voltage to a very low voltage for use in the telecommunications industry. A modification to the standard Forward Resonant...
Show moreIn the field of power electronics there is always a push to create smaller and more efficient power conversion systems. This push is driven by the industry that uses the power systems, and can be realized by new semiconductor devices or new techniques. This examination describes a novel technique for a small and highly efficient method of converting relatively high DC voltage to a very low voltage for use in the telecommunications industry. A modification to the standard Forward Resonant converter results in improvements in component stress, system efficiency, response time, and control circuitry. This examination describes background information needed to understand the concepts in DC to DC power systems, "soft-switching" topologies, and control methods for these systems. The examination introduces several topologies that are currently being used, and several types that have been previously analyzed, as a starting point for the detailed analysis of the proposed converter topology. A detailed analytical analysis is given of the proposed topology, including secondary effects, and component stresses. This analysis is compared to the results found from both Pspice simulation, and a working DC to DC converter. Finally, the topology is examined for potential improvements, and possible refinements to the model described.
Show less - Date Issued
- 2007
- Identifier
- CFE0001960, ucf:47443
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0001960
- Title
- RESONANT ANISOTROPIC EMISSION IN RABBITT SPECTROSCOPY.
- Creator
-
Ghomashi, Bejan M, Argenti, Luca, Douguet, Nicolas, University of Central Florida
- Abstract / Description
-
A variant of RABBITT pump-probe spectroscopy in which the attosecond pulse train comprises both even and odd harmonics of the fundamental IR probe frequency is explored to measure time-resolved photoelectron emission in systems that exhibit autoionizing states. It is shown that the group delay of both one-photon and two-photon resonant transitions is directly encoded in the energy-resolved photoelectron anisotropy as a function of the pump-probe time-delay. This principle is illustrated for a...
Show moreA variant of RABBITT pump-probe spectroscopy in which the attosecond pulse train comprises both even and odd harmonics of the fundamental IR probe frequency is explored to measure time-resolved photoelectron emission in systems that exhibit autoionizing states. It is shown that the group delay of both one-photon and two-photon resonant transitions is directly encoded in the energy-resolved photoelectron anisotropy as a function of the pump-probe time-delay. This principle is illustrated for a 1D model with symmetric zero-range potentials that supports both bound states and shape-resonances. The model is studied using both perturbation theory and solving the time-dependent Schodinger equation on a grid. Moreover, we study the case of a realistic atomic system, helium. In both cases, we demonstrate faithful reconstruction of the phase information for resonant photoemission.
Show less - Date Issued
- 2018
- Identifier
- CFH2000451, ucf:45703
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFH2000451
- Title
- INTEGRATED OPTICAL SPR (SURFACE PLASMON RESONANCE) SENSOR BASED ON OPTOELECTRONIC PLATFORM.
- Creator
-
Bang, Hyungseok, LiKamWa, Patrick, University of Central Florida
- Abstract / Description
-
Current major demands in SPR sensor development are system miniaturization and throughput improvement. Structuring an array of integrated optical SPR sensor heads on a semiconductor based optoelectronic platform could be a promising solution for those issues, since integrated optical waveguides have highly miniaturized dimension and the optoelectronic platform enables on-chip optical-to-electrical signal conversion. Utilizing a semiconductor based platform to achieve optoelectronic...
Show moreCurrent major demands in SPR sensor development are system miniaturization and throughput improvement. Structuring an array of integrated optical SPR sensor heads on a semiconductor based optoelectronic platform could be a promising solution for those issues, since integrated optical waveguides have highly miniaturized dimension and the optoelectronic platform enables on-chip optical-to-electrical signal conversion. Utilizing a semiconductor based platform to achieve optoelectronic functionality poses requirements to the senor head; the sensor head needs to have reasonably small size while it should have reasonable sensitivity and fabrication tolerance. This research proposes a novel type of SPR sensor head and demonstrates a fabricated device with an array of integrated optical SPR sensor heads endowed with optoelectronic functionality. The novel integrated optical SPR sensor head relies on mode conversion efficiency for its operational principle. The beauty of this type of sensor head is it can produce clear contrast in SPR spectrum with a highly miniaturized and simple structure, in contrast to several-millimeter-scale conventional absorption type or interferometer type sensor heads. The integrated optical SPR sensor with optoelectronic functionality has been realized by structuring a dielectric waveguide based SPR sensor head on a photodetector-integrated semiconductor substrate. A large number of unit sensors have been fabricated on a substrate with a batch fabrication process, which promises a high throughput SPR sensor system or low-priced disposable sensors.
Show less - Date Issued
- 2008
- Identifier
- CFE0002312, ucf:47841
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0002312
- Title
- Spin and Charge Transport in Graphene Based Devices.
- Creator
-
Anguera Antonana, Marta, Del Barco, Enrique, Peale, Robert, Bhattacharya, Aniket, Schoenfeld, Winston, University of Central Florida
- Abstract / Description
-
The present dissertation is comprehended in two main parts. The first part is focused on understanding the mechanisms behind spin current to charge current interconversion (i.e. the spin Hall angle), where the spin current is generated by means of spin pumping. The measurement of a positive spin Hall angle of magnitude 0.004 in Uranium is reported in Chapter 2. These results support the idea that the electronic configuration may be at least as important as the atomic number in governing spin...
Show moreThe present dissertation is comprehended in two main parts. The first part is focused on understanding the mechanisms behind spin current to charge current interconversion (i.e. the spin Hall angle), where the spin current is generated by means of spin pumping. The measurement of a positive spin Hall angle of magnitude 0.004 in Uranium is reported in Chapter 2. These results support the idea that the electronic configuration may be at least as important as the atomic number in governing spin Hall effects. In Chapter 3, the design of a spintronics device designed to interconvert charge and spin currents in CVD graphene is presented. The second part of the thesis is centered in the study of transport through single molecules with the use of three-terminal devices. The first evidence of a molecular double quantum dot is detailed in Chapter 5. The conclusions are supported by self-assembled monolayers (SAMs) and single-electron transistors (SETs) measurements. Using gold electrodes for SETs measurements has its disadvantages, two of the main ones being: the junctions are not stable at room temperature and it does not allow for transport measurements in the presence of light. Graphene electrodes, on the other hand, have been reported to be stable at temperatures above room temperature and have no absorption in the visible range. Along those lines, the development of a multilayer graphene-based SET is reported in Chapter 6. Finally, a new technique, based on CVD graphene transistors, that will allow three-terminal measurements on an STM is described in Chapter 7.
Show less - Date Issued
- 2017
- Identifier
- CFE0006715, ucf:51897
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006715
- Title
- Synthesis, Characterization And Antibacterial Activity Of Silver Embedded Silica Nanoparticle/Nanogel Formulation.
- Creator
-
Menezes, Roseline, Santra, Swadeshmukul, Naser, Saleh, Self, William, University of Central Florida
- Abstract / Description
-
The antibacterial property of silver (Ag) has been known since ancient time. It is reported in the literature that silver nanoparticles (AgNPs) exhibit improved antibacterial properties in comparison to silver ions of equivalent metallic Ag concentration. Such improvement in antibacterial activities is due to the high surface area to volume ratio of AgNPs (which facilitates interaction with the bacterial cells), increased release of silver ions and direct intra-cellular uptake of AgNPs...
Show moreThe antibacterial property of silver (Ag) has been known since ancient time. It is reported in the literature that silver nanoparticles (AgNPs) exhibit improved antibacterial properties in comparison to silver ions of equivalent metallic Ag concentration. Such improvement in antibacterial activities is due to the high surface area to volume ratio of AgNPs (which facilitates interaction with the bacterial cells), increased release of silver ions and direct intra-cellular uptake of AgNPs leading to localized release of Ag ions. To date, over 300 consumer products containing AgNPs are available in the market and the inventory is rapidly expanding. The antibacterial efficacy is related to the loading of AgNPs (which controls availability of active Ag ions). It is perhaps challenging to increase AgNPs loading in consumer products without compromising its aesthetic appearance. AgNPs exhibit yellow-brown color due to strong Surface Plasmon Resonance (SPR) absorption; and therefore, it is expected that an increase in loading would change the color of AgNP-containing materials. For applications, such as creating a fast-acting touch-safe surface, higher loading of AgNPs is desirable. It is also desirable to obtain a non-color forming surface. To meet the demands of desirable higher loading of AgNPs and non-color forming surface, the objective of this study is to minimize SPR by engineering Ag containing nanomaterials for potential fast-acting spray-based applications. Within this thesis several reports have been made including synthesis, characterization and antibacterial properties of Ag-loaded silica nanoparticle/nanogel (AgSiNP/NG) material containing nanoformulations. The effects of nanoformulation pH and metallic Ag content on the SPR absorption and antibacterial properties have been studied. The AgSiNP/NG materials were synthesized using silica sol-gel technique at room temperature in water. The color formation of the AgSiNP/NG material was found to be dependent on silver ion loading (15.4 wt% and 42.3 wt %) as well as on the pH (pH 4.0 and pH 7.0). A number of material characterization techniques such as HRTEM, SEM and AFM were used to characterize particle size, crystalline and surface morphology in dry state. Dynamic light scattering (DLS) technique was used to characterize particle size and size distribution in solution. UV-VIS spectroscopy technique was applied to characterize Ag ions and AgNPs in the AgSiNP/NG material. Antibacterial studies were conducted against gram negative E.coli and gram positive B.subtilis and S.aureus. A number of qualitative (well diffusion, BacLightTM live-dead(&)#174; viability) and quantitative (turbidity, resazurin viability) assays were used for antibacterial studies. It was observed that lower pH and low Ag loading minimized SPR absorption, resulting in no yellow-brown color formation. The HRTEM confirmed the formation of ~5-25 nm size highly crystalline AgNPs which were coated with dielectric silica layer (silica gel). AFM, SEM and DLS studies confirmed formation of AgSiNPs in the range between 100 nm (-) 200 nm. The AgSiNP/NG material was effective against both gram-negative and gram-positive bacteria. Based on this research it is suggested that by coating AgNPs with a dielectric material (such as silica); it is possible to suppress SPR absorption.
Show less - Date Issued
- 2011
- Identifier
- CFE0004483, ucf:49308
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004483
- Title
- Thermally annealled plasmonic nanostructures.
- Creator
-
Wang, Chaoming, Su, Ming, Coffey, Kevin, Chai, Xinqing, Schelling, Patrick, University of Central Florida
- Abstract / Description
-
Localized surface plasmon resonance (LSPR) is induced in metal nanoparticles by resonance between incident photons and conduction electrons in nanoparticles. For noble metal nanoparticles, LSPR can lead to strong absorbance of ultraviolet-violet light. Although it is well known that LSPR depends on the size and shape of nanoparticles, the inter-particle spacing, the dielectric properties of metal and the surrounding medium, the temperature dependence of LSPR is not well understood. By...
Show moreLocalized surface plasmon resonance (LSPR) is induced in metal nanoparticles by resonance between incident photons and conduction electrons in nanoparticles. For noble metal nanoparticles, LSPR can lead to strong absorbance of ultraviolet-violet light. Although it is well known that LSPR depends on the size and shape of nanoparticles, the inter-particle spacing, the dielectric properties of metal and the surrounding medium, the temperature dependence of LSPR is not well understood. By thermally annealing gold nanoparticle arrays formed by nanosphere lithography, a shift of LSPR peak upon heating has been shown. The thermal characteristics of the plasmonic nanoparticles have been further used to detect chemicals such as explosive and mercury vapors, which allow direct visual observation of the presence of mercury vapor, as well as thermal desorption measurements.
Show less - Date Issued
- 2012
- Identifier
- CFE0004454, ucf:49322
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004454
- Title
- Wavelength scale resonant structures for integrated photonic applications.
- Creator
-
Weed, Matthew, Schoenfeld, Winston, Moharam, M., Likamwa, Patrick, Delfyett, Peter, Leuenberger, Michael, University of Central Florida
- Abstract / Description
-
An approach to integrated frequency-comb filtering is presented, building from a background in photonic crystal cavity design and fabrication. Previous work in the development of quantum information processing devices through integrated photonic crystals consists of photonic band gap engineering and methods of on-chip photon transfer. This work leads directly to research into coupled-resonator optical waveguides which stands as a basis for the primary line of investigation. These coupled...
Show moreAn approach to integrated frequency-comb filtering is presented, building from a background in photonic crystal cavity design and fabrication. Previous work in the development of quantum information processing devices through integrated photonic crystals consists of photonic band gap engineering and methods of on-chip photon transfer. This work leads directly to research into coupled-resonator optical waveguides which stands as a basis for the primary line of investigation. These coupled cavity systems offer the designer slow light propagation which increases photon lifetime, reduces size limitations toward on-chip integration, and offers enhanced light-matter interaction. A unique resonant structure explained by various numerical models enables comb-like resonant clusters in systems that otherwise have no such regular resonant landscape (e.g. photonic crystal cavities). Through design, simulation, fabrication and test, the work presented here is a thorough validation for the future potential of coupled-resonator filters in frequency comb laser sources.
Show less - Date Issued
- 2013
- Identifier
- CFE0004957, ucf:49568
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004957
- Title
- A NEW QUASI RESONANT DC-LINK FOR PHOTOVOLTAIC MICRO-INVERTERS.
- Creator
-
Grishina, Anna, Batarseh, Issa, Shen, Zheng, Kutkut, Nasser, University of Central Florida
- Abstract / Description
-
PV Inverters have the task of tracking the maximum power point (MPP), and regulating the solar energy generation to this optimal operation point. The second task is the conversion of direct current produced by the solar modules into alternating current compatible with the grid.A new inverter approach such as a single phase micro inverter is emerging aimed to overcome some of the challenges of centralized inverters. As a counterpart to the central inverter, a micro inverter is a small compact...
Show morePV Inverters have the task of tracking the maximum power point (MPP), and regulating the solar energy generation to this optimal operation point. The second task is the conversion of direct current produced by the solar modules into alternating current compatible with the grid.A new inverter approach such as a single phase micro inverter is emerging aimed to overcome some of the challenges of centralized inverters. As a counterpart to the central inverter, a micro inverter is a small compact module attached directly to each solar panel.To provide for the constantly increasing demand for a small size, light weight and high efficiency micro inverter, soft switching power conversion technologies have been employed. The switching stress can be minimized by turning on/off each switch when the voltage across it or the current through it is zero at the switching transition. With the addition of auxiliary circuits such as auxiliary switches and LC resonant components the so called soft switching condition can be achieved for semiconductor devices.Four main purposes to investigate the soft switching technologies for single-phase micro-inverter are:(1) to improve overall efficiency by creating the favorable operating conditions for power devices using soft-switching techniques;(2) to shrink the reactive components by pushing the switching frequency to a higher range with decent efficiency.(3) to ensure soft switching does not exacerbate inverter performance, meaning all conventional PWM algorithms can be applied in order to meet IEEE standards.(4) to investigate which soft switching techniques offer the cheapest topology and control strategy as cost and simple control are crucial for low power inverter applications.An overview on the existing soft-switching inverter topologies for single phase inverter technology is summarized.A new quasi resonant DC link that allows for pulse- width- modulation (PWM) is presented in this thesis. The proposed quasi resonant DC link provides zero-voltage switching (ZVS) condition for the main devices by resonating the DC-link voltage to zero via three auxiliary switches and LC components. The operating principle and mode analysis are given. The simulation was carried out to verify the proposed soft switching technique. A 150W 120VAC single-phase prototype was built. The experimental results show that the soft switching for four main switches can be realized under different load conditions and the peak efficiency can reach 95.6%. The proposed quasi DC link can be applied to both single-phase and three-phase DC/AC micro inverter.In order to boost efficiency and increase power density it is important to evaluate the power loss mechanism in each stage of operation of the micro inverter. Using the datasheet parameters of the commercially available semiconductor switches, conduction and switching losses were estimated. This thesis presents a method to analyze power losses of the new resonant DC link inverter which alleviates topology optimization and MOSFET selection. An analytical, yet simple model for calculating the conduction and switching losses was developed. With this model a rough calculation of efficiency can be done, which helps to speed up the design process and to increase efficiency.
Show less - Date Issued
- 2012
- Identifier
- CFE0004379, ucf:49397
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004379
- Title
- The Relationship Between DNA's Physical Properties and the DNA Molecule's Harmonic Signature, and Related Motion in Water--A Computational Investigation.
- Creator
-
Boyer, Victor, Proctor, Michael, Thompson, William, Karwowski, Waldemar, Calloway, Richard, University of Central Florida
- Abstract / Description
-
This research investigates through computational methods whether the physical properties of DNA contribute to its harmonic signature, the uniqueness of that signature if present, and motion of the DNA molecule in water. When DNA is solvated in water at normal 'room temperature', it experiences a natural vibration due to the Brownian motion of the particles in the water colliding with the DNA. The null hypothesis is that there is no evidence to suggest a relationship between DNA's motion and...
Show moreThis research investigates through computational methods whether the physical properties of DNA contribute to its harmonic signature, the uniqueness of that signature if present, and motion of the DNA molecule in water. When DNA is solvated in water at normal 'room temperature', it experiences a natural vibration due to the Brownian motion of the particles in the water colliding with the DNA. The null hypothesis is that there is no evidence to suggest a relationship between DNA's motion and strand length, while the alternative hypothesis is that there is evidence to suggest a relationship between DNA's vibrational motion and strand length. In a similar vein to the first hypothesis, a second hypothesis posits that DNA's vibrational motion may be dependent on strand content. The nature of this relationship, whether linear, exponential, logarithmic or non-continuous is not hypothesized by this research but will be discovered by testing if there is evidence to suggest a relationship between DNA's motion and strand length. The research also aims to discover whether the motion of DNA, when it varies by strand length and/or content, is sufficiently unique to allow that DNA to be identified in the absence of foreknowledge of the type of DNA that is present in a manner similar to a signature. If there is evidence to suggest that there is a uniqueness in DNA's vibrational motion under varying DNA strand content or length, then additional experimentation will be needed to determine whether these variances are unique across small changes as well as large changes, or large changes only. Finally, the question of whether it might be possible to identify a strand of unique DNA by base pair configuration solely from its vibrational signature, or if not, whether it might be possible to identify changes existing inside of a known DNA strand (such as a corruption, transposition or mutational error) is explored. Given the computational approach to this research, the NAMD simulation package (released by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign) with the CHARMM force field would be the most appropriate set of tools for this investigation (Phillips et al., 2005), and will therefore be the toolset used in this research. For visualization and manipulation of model data, the VMD (Visual Molecular Dynamics) package will be employed. Further, these tools may be optimized and/or be aware of nucleic acid structures, and are free. These tools appear to be sufficient for this task, with validated fidelity of the simulation to provide vibrational and pressure profile data that could be analyzed; sufficient capabilities to do what is being asked of it; speed, so that runs can be done in a reasonable period of time (weeks versus months); and parallelizability, so that the tool could be run over a clustered network of computers dedicated to the task to increase the speed and capacity of the simulations. The computer cluster enabled analysis of 30,000 to 40,000 atom systems spending more than 410,000 CPU computational hours of hundreds of nano second duration, experimental runs each sampled 500,000 times with two-femtosecond (")frames.(")Using Fourier transforms of run pressure readings into frequencies, the simulation investigation could not reject the null hypotheses that the frequencies observed in the system runs are independent on the DNA strand length or content being studied. To be clear, frequency variations were present in the in silicon replications of the DNA in ionized solutions, but we were unable to conclude that those variations were not due to other system factors. There were several tests employed to determine alternative factors that caused these variations. Chief among the factors is the possibility that the water box itself is the source of a large amount of vibrational noise that makes it difficult or impossible with the tools that we had at our disposal to isolate any signals emitted by the DNA strands. Assuming the water-box itself was a source of large amounts of vibrational noise, an emergent hypothesis was generated and additional post-hoc testing was undertaken to attempt to isolate and then filter the water box noise from the rest of the system frequencies. With conclusive results we found that the water box is responsible for the majority of the signals being recorded, resulting in very low signal amplitudes from the DNA molecules themselves. Using these low signal amplitudes being emitted by the DNA, we could not be conclusively uniquely associate either DNA length or content with the remaining observed frequencies. A brief look at a future possible isolation technique, wavelet analysis, was conducted. Finally, because these results are dependent on the tools at our disposal and hence by no means conclusive, suggestions for future research to expand on and further test these hypothesis are made in the final chapter.
Show less - Date Issued
- 2015
- Identifier
- CFE0005930, ucf:50835
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0005930
