VictorJuiz/thesis huggingface dataset:
Capacitive micromachined ultrasonic transducer (CMUT) for chemical detection in air [electronic resource]

Demand for a highly sensitive, accurate, and portable chemical sensor system has been increasing over the recent years for a wide range of applications. For these applications; resonant chemical sensors based on the mass-loading effect (i.e., gravimetric sensors) with chemical functionalization layers are promising candidates. Among them, a capacitive micromachined ultrasonic transducer (CMUT) is a strong candidate with key advantages: 1) it utilizes a thin resonator backed by a vacuum cavity which results in a high quality factor, 2) it has the ability to apply massive parallelism, thereby, increasing its reliability and lowering the motional impedance, and 3) consistent repeatability and reliability in the fabrication process. The development of a CMUT-based chemical sensor encompasses device selection and characterization, oscillation circuit design and implementation, chemical functionalization, and a chemical test. CMUTs with a resonant frequency ranging from 6 MHz to 50 MHz are selected. An oscillation circuit is designed to track the parallel resonant frequency of the CMUT. The CMUT is chemically activated by thin polymer layers (e.g., Polyisobutylene or synthesized polymer) to absorb an analyte of interest. Chemical experimentation reveals that the CMUT-based chemical sensor has a high sensitivity, the capability of analyte identification, and a reliable operation. In order to improve the performance of the CMUT as a mass-loading sensor, the device should have the following elements: a thin plate with a high frequency, low parasitic capacitance, low operating voltage, and a high breakdown voltage. The local oxidation of silicon/wafer-bonding (LOCOS/wafer-bonding) process meets this criteria. The process realizes a CMUT with a quality factor of 400 in air, a resonant frequency up to 50 MHz, and an unprecedented small gap of 40-nm. This thesis presents a highly sensitive chemical sensor based on the CMUT technology with theoretical mass sensitivities of 54.4 zg/Hz/um^2 for the devices operating at 50 MHz. The multi-resonator configuration is more reliable in operation and makes the oscillator circuit easier to design. Since the oscillator circuit was designed with low-frequency (0.2 Hz) noise and an equivalent volume resolution of 21 ppt of Dimethyl methylphosphonate (DMMP); a simulant of Sarin (GB) was achieved. This work thus demonstrates that CMUT technology has great potential for the implementation of chemical sensing systems that are sensitive; yet reliable and portable.

Keywords: Mechanical Engineering
Advisor: Kenny Thomas William primary advisor. Thesis advisor
Khuri-Yakub Butrus T.
Howe Roger Thomas advisor. Thesis advisor
Capacity investment strategies for environmentally responsible firms [electronic resource]

This thesis consists of three essays that analyze the capacity investment strategies for environmentally responsible firms, firms that introduce products into the market which have less impact on the environment or are less harmful to human health than their traditional equivalents, or firms that operate with conventional methods but switch to less carbon-intensive technologies in their new capacity investments due to the climate regulations. In the first essay (co-authored with Erica L. Plambeck), we examine capacity leadership, in which a manufacturer adjusts the timing and level of her own capacity investment in order to motivate noncontractible capacity investment by a supplier. When the firms have common information about the demand distribution and their capacities are complements, the manufacturer can increase the supplier's incentive for capacity investment by building her own capacity early. When the supplier's bargaining strength is moderately high, early capacity investment by the manufacturer strictly increases both firms' expected profits. The manufacturer's optimal level of early capacity increases as the selling price and demand for the end product increase, capacity costs decrease, or she obtains private information that demand is likely to be high. If the supplier's capacity investment is contractible, the manufacturer may still achieve greater expected profit through early capacity investment than a contract. When the firms' capacities are substitutes, early capacity investment by the manufacturer reduces her eventual payment to the supplier and thus the supplier's incentive for capacity investment. Nevertheless, the supplier's capacity cost is sufficiently lower than that of the manufacturer, the manufacturer optimally builds early capacity to signal a high demand forecast. These results may help to explain why several manufacturers of renewable energy and energy-efficient products have built capacity early, before it could be utilized. In the second essay (co-authored with Stefan Reichelstein), we investigate the carbon capture and storage (CCS) technologies for fossil fuel power plants, which offer the potential for significant reductions in carbon dioxide emissions. We examine the break-even value for CCS adoptions, that is, the critical value in the charge for carbon dioxide emissions that would justify investment in CCS capabilities. Our analysis takes explicitly into account that the supply of electricity at the wholesale level (generation) is organized competitively in some U.S. jurisdictions, while in others a regulated utility provides integrated generation and distribution services. For either market structure, we find that emissions charges near 0 per tonne of carbon dioxide would be the break-even value for adopting CCS capabilities at new coal-fired power plants. The corresponding break-even values for natural gas plants are substantially higher, near

Advisor: Plambeck Erica L. primary advisor. Thesis advisor
Lee Hau Leung advisor. Thesis advisor
Weber Thomas advisor. Thesis advisor
Capacity investment strategies for environmentally responsible firms [electronic resource]

This thesis consists of three essays that analyze the capacity investment strategies for environmentally responsible firms, firms that introduce products into the market which have less impact on the environment or are less harmful to human health than their traditional equivalents, or firms that operate with conventional methods but switch to less carbon-intensive technologies in their new capacity investments due to the climate regulations. In the first essay (co-authored with Erica L. Plambeck), we examine capacity leadership, in which a manufacturer adjusts the timing and level of her own capacity investment in order to motivate noncontractible capacity investment by a supplier. When the firms have common information about the demand distribution and their capacities are complements, the manufacturer can increase the supplier's incentive for capacity investment by building her own capacity early. When the supplier's bargaining strength is moderately high, early capacity investment by the manufacturer strictly increases both firms' expected profits. The manufacturer's optimal level of early capacity increases as the selling price and demand for the end product increase, capacity costs decrease, or she obtains private information that demand is likely to be high. If the supplier's capacity investment is contractible, the manufacturer may still achieve greater expected profit through early capacity investment than a contract. When the firms' capacities are substitutes, early capacity investment by the manufacturer reduces her eventual payment to the supplier and thus the supplier's incentive for capacity investment. Nevertheless, the supplier's capacity cost is sufficiently lower than that of the manufacturer, the manufacturer optimally builds early capacity to signal a high demand forecast. These results may help to explain why several manufacturers of renewable energy and energy-efficient products have built capacity early, before it could be utilized. In the second essay (co-authored with Stefan Reichelstein), we investigate the carbon capture and storage (CCS) technologies for fossil fuel power plants, which offer the potential for significant reductions in carbon dioxide emissions. We examine the break-even value for CCS adoptions, that is, the critical value in the charge for carbon dioxide emissions that would justify investment in CCS capabilities. Our analysis takes explicitly into account that the supply of electricity at the wholesale level (generation) is organized competitively in some U.S. jurisdictions, while in others a regulated utility provides integrated generation and distribution services. For either market structure, we find that emissions charges near 0 per tonne of carbon dioxide would be the break-even value for adopting CCS capabilities at new coal-fired power plants. The corresponding break-even values for natural gas plants are substantially higher, near

Keywords: Business.
Advisor: Plambeck Erica L. primary advisor. Thesis advisor
Lee Hau Leung advisor. Thesis advisor
Weber Thomas advisor. Thesis advisor
Carbon nanotube electronics [electronic resource]

In recent years, carbon-based electronics have surfaced as potential candidates for substituting silicon-based logic as scaling continues into the new decade and beyond 20nm technology node. In particular, carbon nanotubes (CNTs) and graphene nanoribbons have received significant attention from the academia as well the industry. Ideal electronic and structural properties of these materials make them suitable for electronic applications. In this work we discuss the basics of CNT growth and device fabrication, explore performance and contact resistance for CNT Field Effect Transistors (CNFETs) based on horizontally-aligned grown CNTs. We provide a physics-based compact model for simulation of CNFETs in a) quantum ballistic and b) semiclassical diffusive regimes. Measuring channel carrier density is essential for extracting key device parameters such as mobility while it can also provide a detailed picture of the underlying quantum mechanics. Since CNTs and nanostructures in general are limited by quantum capacitance, will also provide an Integrated Capacitance Bridge (ICB) for wide temperature-range, high resolution measurements of quantum capacitance in nanostructures with an excitation amplitude smaller than kBT/q.

Keywords: Electrical Engineering
Advisor: Saraswat Krishna primary advisor. Thesis advisor
Wong Hon-Sum Philip
Goldhaber-Gordon David
Carbon nanotube films and microjet cooling devices for thermal management [electronic resource]

The downsizing of electronic devices and the consequent increasing power densities pose thermal management challenges for the semiconductor industry. Since the present thermal solutions limit their cooling capacity, developing new cooling methods for electronic devices has become important. This dissertation presents two types of novel methods for heat dissipation from integrated circuits: One is the use of advanced thermal interface materials, such as carbon nanotubes (CNTs), to increase heat dissipation between the solid and solid surface, such as a chip and heat sink. The second method is the use of a microjet impingement device to improve heat transfer between a liquid and solid in a heat sink. As advanced interface materials, vertically aligned carbon nanotube films are promising because of their unique mechanical and thermal properties. The first part of the dissertation describes the design, fabrication, and testing of CNTs using resonators to characterize their mechanical properties. Discussed in detail is the preparation of carbon nanotubes using different recipes, resulting in varied thicknesses of single-walled carbon nanotube films and multi-walled carbon nanotube films. The measurements of the resonant frequency shifts due to the presence of the CNT films using a laser Doppler vibrometer system result in extracted moduli of 0.5-220 [Mu]m-thick nanotube films varying from 1 to 370 MPa. To show how the physics between the effective modulus and thickness are connected, an analysis for the height dependence of the modulus is provided. After an image analysis is presented, a nanotube dynamics simulation based on tube properties and film morphology is introduced to predict mechanical properties. In addition to discussing the proposed interface materials, the second part of the dissertation describes the design, fabrication and testing of microjet impingement cooling, which display high heat capacities, as an advanced thermal management solution. The design of single-jet and multi-jet arrays with different numbers of diameters, locations, and spacing is discussed. Specifically, this part demonstrates how the microjet hydrodynamics are quantified using two-dimensional images by [Mu]PIV techniques, enabling the reconstruction of the three-dimensional flow field. The results indicate that CNT films offer a mechanical compliance that is suitable for TIM applications and that the microscale liquid jet devices provide quantified flow physics for heat sink applications.

Keywords: Mechanical Engineering
Advisor: Kenny Thomas William primary advisor. Thesis advisor
Goodson Kenneth E.
Pruitt Beth advisor. Thesis advisor
Carbon nanotube transparent electrodes for photovoltaic applications [electronic resource]

Virtually all solar cells require a transparent and conductive (TC) layer on the top surface that allows sunlight to enter the cell and photoexcited charge to be conducted laterally across the top surface. The impact on power conversion efficiency due to reflection, absorption, resistive losses and lost active area is a reduction by 10 -- 25 %, relative. Historically, doped metal oxides such as tin doped indium oxide (ITO) have been used. In the last several years, however, there has been renewed interest in this area with the development of several new nanostructured materials, many of which have the potential for performance, processing, and cost advantages. In the first portion of this work, we describe TC related efficiency losses in detail for the two major categories of solar cells. For thin film monolithically integrated modules, TC related losses can be as high as 25 % and for standard modules of cell strung together losses are typically 10 -- 15 %. For the purpose of developing new TC materials, we specify the material performance requirements for a competitive TC material and show the expected TC related efficiency losses in photovoltaic (PV) modules for any material of known electrical and optical properties. We then provide an overview of the leading nanostructured materials and show that carbon nanotubes (CNT) have basic optoelectronic material properties that are superior to traditional metal oxides. We exhibit the first demonstration of a highly flexible organic solar cell using carbon nanotube films as the TC. The achieved power conversion efficiency of 2.5 % is comparable to the 3.0 % efficiency of the control device using ITO and the flexibility of the CNT device is far greater. Finally, we detail an in-depth investigation of the electrical properties of carbon nanotube networks in order to determine and understand the performance limitations. For this, we develop a novel method of atomic force microscope (AFM) scratch lithography in order to isolate individual CNT bundles and a novel method of electric force microscopy (EFM) in order to quantitatively measure local contact resistances on the nanoscale between CNT bundles. We measure bundle-to-bundle junction resistance for a range of bundle diameters which reveals a previously unobserved inverse scaling of contact resistance with diameter. Values range from 1 kOhm to 200 kOhm for bundle diameters typical of CNT TC networks. We also measure the resistivity of ropes of bundles and we find that this resistance is very high and limits the conductivity of the CNT TC films studied in this work. The structure property relationships revealed from these measurements clearly show what type of morphology control is necessary for high performance CNT TCs and that increasing tube length and/or decreasing junction resistance are the primary routes for further increases in performance.

Keywords: Materials Science and Engineering
Advisor: McGehee Michael
Goldhaber-Gordon David
Peumans Peter
Cardiac development, growth, and disease through chromatin remodeling [electronic resource]

The heart is the first organ to function in development and continues to beat for seventy or more years in an adult's life. Cardiogenesis therefore is no simple task; genes have to be precisely regulated to meet the needs of a developing heart. ATP-dependent chromatin remodeling provides an important mechanism to regulate gene expression. Specifically, Brg1-associated factor, or the BAF, complexes, are crucial in heart development. Endocardial Brg1 represses the expression of a metalloproteinase, ADAMTS1, in order to allow sufficient cardiac jelly expansion for trabecular development. In addition, Brg1 functions in the myocardium to repress VEGFA to prevent the ectopic formation of coronary vasculature from the epicardium in a non-cell autonomous manner. And lastly, Brg1 serves as a bridge linking embryonic development and adult cardiomyopathies. Brg1 functions in the myocardium to keep the cardiomyocytes in a proliferating state through promoting BMP10 and repressing a cyclin-dependent kinase inhibitor p57kip2. Without Brg1, cardiomyocytes cease cell division, mature, and express adult form of myosin heavy (MHC) chain gene. Brg1 is normally turned off in adult life; however, following cardiac stress it is reactivated and turns on embryonic fetal program characterized by re-induction of embryonic MHC expression. Preventing Brg1 re-expression can repress cardiac hypertrophy and restore adult MHC expression. Furthermore, Brg1physically interacts with other chromatin remodeling enzymes such as histone deacetylases and poly-ADP ribose polymerases to control expression of MHC genes and regulate cardiomyocyte differentiation. In all, ATP-dependent chromatin remodeling plays important roles in heart development and disease and may provide a suitable therapeutic target for human cardiomyopathies in the future.

Advisor: Chang Ching-Pin primary advisor. Thesis advisor
Cleary Michael L. advisor. Thesis advisor
Crabtree Gerald R. advisor. Thesis advisor
Kuo Calvin Jay advisor. Thesis advisor
Cationic, random-coil protein polymers for free-solution conjugate electrophoresis (FSCE) in microchannels [electronic resource]

Access to an individual's genetic data, often for a small set of genes, will offer increasing value in medical practice; e.g., in cancer treatment it may be useful to track sequence alterations in oncogenes over time, or even spatially within a tumor. Such applications create a need for rapid, low-cost, scalable technologies for high-accuracy sequencing of human DNA. Some regions of the human genome, particularly repeat-rich loci, are challenging to analyze accurately with short-read, next-gen DNA sequencing technologies. Long-read, high-accuracy sequencing is done now by capillary array electrophoresis (CE), but DNA separations on microdevices are at least 10 times faster and deliver equally long, accurate reads. Free-Solution Conjugate Electrophoresis (FSCE) is a novel method of DNA sequencing ideal for implementation on microfluidic devices, as it obviates the need for viscous polymer solutions to separate DNA. FSCE uses a monodisperse protein "drag-tag", tethered end-on to one terminus of ssDNA fragments, to enable sequencing in free solution. The most difficult aspect of developing FSCE is the creation of long (> 500-amino acid (aa)), totally monodisperse protein drag-tags needed for long reads. Recent studies in FSCE indicated that introducing positive charges in a drag-tag would help to achieve higher hydrodynamic drag without requirements of significantly increasing the size of the drag-tag. In this dissertation, a new family of de novo-designed proteins with intentionally included cationic (Arg) amino acids was designed. A faster and easier purification method combining affinity chromatography and tag-removal was established to create protein polymers with improved monodispersity required for FSCE applications. After rigorous characterization, these novel protein drag-tags were analyzed by free-solution separations and FSCE sequencing. Through these studies, I investigated critical biophysical attributes of positively charged drag-tags important to FSCE performance and identified the limits for inclusion of positive charges in sequences of protein polymer drag-tags for successful FSCE applications. The investigations of two post-Sanger conjugation strategies were also initiated and were proven to enable the utilization of previously unusable larger/higher charged protein drag-tags that suppressed the enzymatic extension when attached to sequencing primers prior to the Sanger reaction.

Keywords: Bioengineering.
Advisor: Barron Annelise E. primary advisor. Thesis advisor
Heilshorn Sarah advisor. Thesis advisor
Swartz James R. advisor. Thesis advisor
Change-point models on point processes and applications in genomics [electronic resource]

In this thesis, we present advancements in some change-point problems and their applications to genomic problems that arises from massively parallel sequencing. Change-point problems are concerned with abrupt changes in the generating distribution of a stochastic process evolving over time, space, or any ordered set. This thesis focuses on a number of change-point models and inference problems on point processes. We provide a change-point model and efficient algorithms to detect change-points in relative intensity of non-homogeneous Poisson processes. A model selection approach is constructed in the spirit of classical Baysian Information Criterion, but tailored to the irregularity of change-point problems. We review an array of inference problems surrounding the change-point construct; and propose a point-wise Bayesian credible interval for the parameter of the generating distribution for exponential family. An asymptotic result on the relationship between frequentist and Baysian change-point estimator is shown. We investigate how data characteristics, such as sample size, signal strength, and change-point location, influences the inference procedures through a simulation study. On the application front, modern massively parallel sequencing generates enormous and rich data with much systematic and random noise. We provide a survey of the sequencing technologies and some statistical challenges in various steps of sequencing data analysis. A recent application of sequencing in population and tumor genomics is the profiling of genome copy number and detection of copy number variations across sample. We demonstrate in this thesis that sequencing reads can be viewed naturally as a stochastic process along the genome. Copy number variants are modeled as abrupt jumps in the read intensity function. This modeling assumption resembles the biological reality of mutations that leads to copy number change. We demonstrate the application of change-point methods on actual sequencing data. Our method is found to compare favorably against a commonly used existing method in a spike-in simulation study. We lastly discuss a direction in which our change-point methods can be extended. It is often of interest to find recurrent copy number variants among a collection of biological samples. We review existing array-based multi-sample copy number profiling methods. Estimation and model selection procedures for the multi-sample sequencing setting are derived as extensions of our two-sample methods. A key challenge is the treatment of carrier status, which is whether a sample carries the recurrent variant of question. We present two sets of methods, one based on the assumption that all samples are carriers and the other based on a known carrier set. The statistical characteristics of the two methods are compared in a number of simulation scenarios.

Keywords: Statistics
Advisor: Zhang Nancy R. (Nancy Ruonan) primary advisor. Thesis advisor
Siegmund David
Wong Wing Hung advisor. Thesis advisor