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Locomotion of microorganisms is commonly observed in nature. Although microorganism locomotion is commonly attributed to mechanical deformation of solid appendages, in 1956 Nobel Laureate Peter Mitchell proposed that an asymmetric ion flux on a bacterium's surface could generate electric fields that drive locomotion via self-electrophoresis. Recent advances in nanofabrication have enabled the engineering of synthetic analogues, bimetallic colloidal particles, that swim due to asymmetric ion flux originally proposed by Mitchell. Bimetallic colloidal particles swim through aqueous solutions by converting chemical fuel to fluid motion through asymmetric electrochemical reactions. This dissertation presents novel bimetallic motor fabrication strategies, motor functionality, and a study of the motor collective behavior in chemical concentration gradients. Brownian dynamics simulations and experiments show that the motors exhibit chemokinesis, a motile response to chemical gradients that results in net migration and concentration of particles. Chemokinesis is typically observed in living organisms and distinct from chemotaxis in that there is no particle directional sensing. The synthetic motor chemokinesis observed in this work is due to variation in the motor's velocity and effective diffusivity as a function of the fuel and salt concentration. Static concentration fields are generated in microfluidic devices fabricated with porous walls. The development of nanoscale particles that swim autonomously and collectively in chemical concentration gradients can be leveraged for a wide range of applications such as directed drug delivery, self-healing materials, and environmental remediation.
ContributorsWheat, Philip Matthew (Author) / Posner, Jonathan D (Thesis advisor) / Phelan, Patrick (Committee member) / Chen, Kangping (Committee member) / Buttry, Daniel (Committee member) / Calhoun, Ronald (Committee member) / Arizona State University (Publisher)
Created2011
Description
Nonlinear dispersive equations model nonlinear waves in a wide range of physical and mathematics contexts. They reinforce or dissipate effects of linear dispersion and nonlinear interactions, and thus, may be of a focusing or defocusing nature. The nonlinear Schrödinger equation or NLS is an example of such equations. It appears as a model in hydrodynamics, nonlinear optics, quantum condensates, heat pulses in solids and various other nonlinear instability phenomena. In mathematics, one of the interests is to look at the wave interaction: waves propagation with different speeds and/or different directions produces either small perturbations comparable with linear behavior, or creates solitary waves, or even leads to singular solutions. This dissertation studies the global behavior of finite energy solutions to the $d$-dimensional focusing NLS equation, $i partial _t u+Delta u+ |u|^{p-1}u=0, $ with initial data $u_0in H^1,; x in Rn$; the nonlinearity power $p$ and the dimension $d$ are chosen so that the scaling index $s=frac{d}{2}-frac{2}{p-1}$ is between 0 and 1, thus, the NLS is mass-supercritical $(s>0)$ and energy-subcritical $(s<1).$ For solutions with $ME[u_0]<1$ ($ME[u_0]$ stands for an invariant and conserved quantity in terms of the mass and energy of $u_0$), a sharp threshold for scattering and blowup is given. Namely, if the renormalized gradient $g_u$ of a solution $u$ to NLS is initially less than 1, i.e., $g_u(0)<1,$ then the solution exists globally in time and scatters in $H^1$ (approaches some linear Schr"odinger evolution as $ttopminfty$); if the renormalized gradient $g_u(0)>1,$ then the solution exhibits a blowup behavior, that is, either a finite time blowup occurs, or there is a divergence of $H^1$ norm in infinite time. This work generalizes the results for the 3d cubic NLS obtained in a series of papers by Holmer-Roudenko and Duyckaerts-Holmer-Roudenko with the key ingredients, the concentration compactness and localized variance, developed in the context of the energy-critical NLS and Nonlinear Wave equations by Kenig and Merle. One of the difficulties is fractional powers of nonlinearities which are overcome by considering Besov-Strichartz estimates and various fractional differentiation rules.
ContributorsGuevara, Cristi Darley (Author) / Roudenko, Svetlana (Thesis advisor) / Castillo_Chavez, Carlos (Committee member) / Jones, Donald (Committee member) / Mahalov, Alex (Committee member) / Suslov, Sergei (Committee member) / Arizona State University (Publisher)
Created2011
Description
In this thesis the performance of a Hybrid AC System (HACS) is modeled and optimized. The HACS utilizes solar photovoltaic (PV) panels to help reduce the demand from the utility during peak hours. The system also includes an ice Thermal Energy Storage (TES) tank to accumulate cooling energy during off-peak hours. The AC runs continuously on grid power during off-peak hours to generate cooling for the house and to store thermal energy in the TES. During peak hours, the AC runs on the power supplied from the PV, and cools the house along with the energy stored in the TES. A higher initial cost is expected due to the additional components of the HACS (PV and TES), but a lower operational cost due to higher energy efficiency, energy storage and renewable energy utilization. A house cooled by the HACS will require a smaller size AC unit (about 48% less in the rated capacity), compared to a conventional AC system. To compare the cost effectiveness of the HACS with a regular AC system, time-of-use (TOU) utility rates are considered, as well as the cost of the system components and the annual maintenance. The model shows that the HACS pays back its initial cost of $28k in about 6 years with an 8% APR, and saves about $45k in total cost when compared to a regular AC system that cools the same house for the same period of 6 years.
ContributorsJubran, Sadiq (Author) / Phelan, Patrick (Thesis advisor) / Calhoun, Ronald (Committee member) / Trimble, Steve (Committee member) / Arizona State University (Publisher)
Created2011
Description
While much effort in Stirling engine development is placed on making the high-temperature region of the Stirling engine warmer, this research explores methods to lower the temperature of the cold region by improving heat transfer in the cooler. This paper presents heat transfer coefficients obtained for a Stirling engine heat exchanger with oscillatory flow. The effects of oscillating frequency and input heat rate on the heat transfer coefficients are evaluated and details on the design and development of the heat exchanger test apparatus are also explained. Featured results include the relationship between overall heat transfer coefficients and oscillation frequency which increase from 21.5 to 46.1 Wm-2K-1 as the oscillation frequency increases from 6.0 to 19.3 Hz. A correlation for the Nusselt number on the inside of the heat exchange tubes in oscillatory flow is presented in a concise, dimensionless form in terms of the kinetic Reynolds number as a result of a statistical analysis. The test apparatus design is proven to be successful throughout its implementation due to the usefulness of data and clear trends observed. The author is not aware of any other publicly-available research on a Stirling engine cooler to the extent presented in this paper. Therefore, the present results are analyzed on a part-by-part basis and compared to segments of other research; however, strong correlations with data from other studies are not expected. The data presented in this paper are part of a continuing effort to better understand heat transfer properties in Stirling engines as well as other oscillating flow applications.
ContributorsEppard, Erin (Author) / Phelan, Patrick (Thesis advisor) / Trimble, Steve (Committee member) / Calhoun, Ronald (Committee member) / Arizona State University (Publisher)
Created2011
Description
Multiphase flows are an important part of many natural and technological phe- nomena such as ocean-air coupling (which is important for climate modeling) and the atomization of liquid fuel jets in combustion engines. The unique challenges of multiphase flow often make analytical solutions to the governing equations impos- sible and experimental investigations very difficult. Thus, high-fidelity numerical simulations can play a pivotal role in understanding these systems. This disserta- tion describes numerical methods developed for complex multiphase flows and the simulations performed using these methods. First, the issue of multiphase code verification is addressed. Code verification answers the question "Is this code solving the equations correctly?" The method of manufactured solutions (MMS) is a procedure for generating exact benchmark solutions which can test the most general capabilities of a code. The chief obstacle to applying MMS to multiphase flow lies in the discontinuous nature of the material properties at the interface. An extension of the MMS procedure to multiphase flow is presented, using an adaptive marching tetrahedron style algorithm to compute the source terms near the interface. Guidelines for the use of the MMS to help locate coding mistakes are also detailed. Three multiphase systems are then investigated: (1) the thermocapillary motion of three-dimensional and axisymmetric drops in a confined apparatus, (2) the flow of two immiscible fluids completely filling an enclosed cylinder and driven by the rotation of the bottom endwall, and (3) the atomization of a single drop subjected to a high shear turbulent flow. The systems are simulated numerically by solving the full multiphase Navier- Stokes equations coupled to the various equations of state and a level set interface tracking scheme based on the refined level set grid method. The codes have been parallelized using MPI in order to take advantage of today's very large parallel computational architectures. In the first system, the code's ability to handle surface tension and large tem- perature gradients is established. In the second system, the code's ability to sim- ulate simple interface geometries with strong shear is demonstrated. In the third system, the ability to handle extremely complex geometries and topology changes with strong shear is shown.
ContributorsBrady, Peter, Ph.D (Author) / Herrmann, Marcus (Thesis advisor) / Lopez, Juan (Thesis advisor) / Adrian, Ronald (Committee member) / Calhoun, Ronald (Committee member) / Chen, Kangping (Committee member) / Arizona State University (Publisher)
Created2011
Description
Thermal interface materials (TIMs) are extensively used in thermal management applications especially in the microelectronics industry. With the advancement in microprocessors design and speed, the thermal management is becoming more complex. With these advancements in microelectronics, there have been parallel advancements in thermal interface materials. Given the vast number of available TIM types, selection of the material for each specific application is crucial. Most of the metrologies currently available on the market are designed to qualify TIMs between two perfectly flat surfaces, mimicking an ideal scenario. However, in realistic applications parallel surfaces may not be the case. In this study, a unique characterization method is proposed to address the need for TIMs characterization between non-parallel surfaces. Two different metrologies are custom-designed and built to measure the impact of tilt angle on the performance of TIMs. The first metrology, Angular TIM Tester, is based on the ASTM D5470 standard with flexibility to perform characterization of the sample under induced tilt angle of the rods. The second metrology, Bare Die Tilting Metrology, is designed to validate the performance of TIM under induced tilt angle between the bare die and the cooling solution in an "in-situ" package testing format. Several types of off-the-shelf thermal interface materials were tested and the results are outlined in the study. Data were collected using both metrologies for all selected materials. It was found that small tilt angles, up to 0.6°, have an impact on thermal resistance of all materials especially for in-situ testing. In addition, resistance change between 0° and the selected tilt angle was found to be in close agreement between the two metrologies for paste-based materials and phase-change material. However, a clear difference in the thermal performance of the tested materials was observed between the two metrologies for the gap filler materials.
ContributorsHarris, Enisa (Author) / Phelan, Patrick (Thesis advisor) / Calhoun, Ronald (Committee member) / Devasenathipathy, Shankar (Committee member) / Arizona State University (Publisher)
Created2011
Description
The flow around a golf ball is studied using direct numerical simulation (DNS). An immersed boundary approach is adopted in which the incompressible Navier-Stokes equations are solved using a fractional step method on a structured, staggered grid in cylindrical coordinates. The boundary conditions on the surface are imposed using momentum forcing in the vicinity of the boundary. The flow solver is parallelized using a domain decomposition strategy and message passing interface (MPI), and exhibits linear scaling on as many as 500 processors. A laminar flow case is presented to verify the formal accuracy of the method. The immersed boundary approach is validated by comparison with computations of the flow over a smooth sphere. Simulations are performed at Reynolds numbers of 2.5 × 104 and 1.1 × 105 based on the diameter of the ball and the freestream speed and using grids comprised of more than 1.14 × 109 points. Flow visualizations reveal the location of separation, as well as the delay of complete detachment. Predictions of the aerodynamic forces at both Reynolds numbers are in reasonable agreement with measurements. Energy spectra of the velocity quantify the dominant frequencies of the flow near separation and in the wake. Time-averaged statistics reveal characteristic physical patterns in the flow as well as local trends within dimples. A mechanism of drag reduction due to the dimples is confirmed, and metrics for dimple optimization are proposed.
ContributorsSmith, Clinton E (Author) / Squires, Kyle D (Thesis advisor) / Balaras, Elias (Committee member) / Herrmann, Marcus (Committee member) / Adrian, Ronald (Committee member) / Stanzione, Daniel C (Committee member) / Calhoun, Ronald (Committee member) / Arizona State University (Publisher)
Created2011
Description
Pathogenic Gram-negative bacteria employ a variety of molecular mechanisms to combat host defenses. Two-component regulatory systems (TCR systems) are the most ubiquitous signal transduction systems which regulate many genes required for virulence and survival of bacteria. In this study, I analyzed different TCR systems in two clinically-relevant Gram-negative bacteria, i.e., oral pathogen Porphyromonas gingivalis and enterobacterial Escherichia coli. P. gingivalis is a major causative agent of periodontal disease as well as systemic illnesses, like cardiovascular disease. A microarray study found that the putative PorY-PorX TCR system controls the secretion and maturation of virulence factors, as well as loci involved in the PorSS secretion system, which secretes proteinases, i.e., gingipains, responsible for periodontal disease. Proteomic analysis (SILAC) was used to improve the microarray data, reverse-transcription PCR to verify the proteomic data, and primer extension assay to determine the promoter regions of specific PorX regulated loci. I was able to characterize multiple genetic loci regulated by this TCR system, many of which play an essential role in hemagglutination and host-cell adhesion, and likely contribute to virulence in this bacterium. Enteric Gram-negative bacteria must withstand many host defenses such as digestive enzymes, low pH, and antimicrobial peptides (AMPs). The CpxR-CpxA TCR system of E. coli has been extensively characterized and shown to be required for protection against AMPs. Most recently, this TCR system has been shown to up-regulate the rfe-rff operon which encodes genes involved in the production of enterobacterial common antigen (ECA), and confers protection against a variety of AMPs. In this study, I utilized primer extension and DNase I footprinting to determine how CpxR regulates the ECA operon. My findings suggest that CpxR modulates transcription by directly binding to the rfe promoter. Multiple genetic and biochemical approaches were used to demonstrate that specific TCR systems contribute to regulation of virulence factors and resistance to host defenses in P. gingivalis and E. coli, respectively. Understanding these genetic circuits provides insight into strategies for pathogenesis and resistance to host defenses in Gram negative bacterial pathogens. Finally, these data provide compelling potential molecular targets for therapeutics to treat P. gingivalis and E. coli infections.
ContributorsLeonetti, Cori (Author) / Shi, Yixin (Thesis advisor) / Stout, Valerie (Committee member) / Nickerson, Cheryl (Committee member) / Sandrin, Todd (Committee member) / Arizona State University (Publisher)
Created2013
Description
The study of bacterial resistance to antimicrobial peptides (AMPs) is a significant area of interest as these peptides have the potential to be developed into alternative drug therapies to combat microbial pathogens. AMPs represent a class of host-mediated factors that function to prevent microbial infection of their host and serve as a first line of defense. To date, over 1,000 AMPs of various natures have been predicted or experimentally characterized. Their potent bactericidal activities and broad-based target repertoire make them a promising next-generation pharmaceutical therapy to combat bacterial pathogens. It is important to understand the molecular mechanisms, both genetic and physiological, that bacteria employ to circumvent the bactericidal activities of AMPs. These understandings will allow researchers to overcome challenges posed with the development of new drug therapies; as well as identify, at a fundamental level, how bacteria are able to adapt and survive within varied host environments. Here, results are presented from the first reported large scale, systematic screen in which the Keio collection of ~4,000 Escherichia coli deletion mutants were challenged against physiologically significant AMPs to identify genes required for resistance. Less than 3% of the total number of genes on the E. coli chromosome was determined to contribute to bacterial resistance to at least one AMP analyzed in the screen. Further, the screen implicated a single cellular component (enterobacterial common antigen, ECA) and a single transporter system (twin-arginine transporter, Tat) as being required for resistance to each AMP class. Using antimicrobial resistance as a tool to identify novel genetic mechanisms, subsequent analyses were able to identify a two-component system, CpxR/CpxA, as a global regulator in bacterial resistance to AMPs. Multiple previously characterized CpxR/A members, as well as members found in this study, were identified in the screen. Notably, CpxR/A was found to transcriptionally regulate the gene cluster responsible for the biosynthesis of the ECA. Thus, a novel genetic mechanism was uncovered that directly correlates with a physiologically significant cellular component that appears to globally contribute to bacterial resistance to AMPs.
ContributorsWeatherspoon-Griffin, Natasha (Author) / Shi, Yixin (Thesis advisor) / Clark-Curtiss, Josephine (Committee member) / Misra, Rajeev (Committee member) / Nickerson, Cheryl (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2013
Description
This thesis outlines the development of a vector retrieval technique, based on data assimilation, for a coherent Doppler LIDAR (Light Detection and Ranging). A detailed analysis of the Optimal Interpolation (OI) technique for vector retrieval is presented. Through several modifications to the OI technique, it is shown that the modified technique results in significant improvement in velocity retrieval accuracy. These modifications include changes to innovation covariance portioning, covariance binning, and analysis increment calculation. It is observed that the modified technique is able to make retrievals with better accuracy, preserves local information better, and compares well with tower measurements. In order to study the error of representativeness and vector retrieval error, a lidar simulator was constructed. Using the lidar simulator a thorough sensitivity analysis of the lidar measurement process and vector retrieval is carried out. The error of representativeness as a function of scales of motion and sensitivity of vector retrieval to look angle is quantified. Using the modified OI technique, study of nocturnal flow in Owens' Valley, CA was carried out to identify and understand uncharacteristic events on the night of March 27th 2006. Observations from 1030 UTC to 1230 UTC (0230 hr local time to 0430 hr local time) on March 27 2006 are presented. Lidar observations show complex and uncharacteristic flows such as sudden bursts of westerly cross-valley wind mixing with the dominant up-valley wind. Model results from Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS®) and other in-situ instrumentations are used to corroborate and complement these observations. The modified OI technique is used to identify uncharacteristic and extreme flow events at a wind development site. Estimates of turbulence and shear from this technique are compared to tower measurements. A formulation for equivalent wind speed in the presence of variations in wind speed and direction, combined with shear is developed and used to determine wind energy content in presence of turbulence.
ContributorsChoukulkar, Aditya (Author) / Calhoun, Ronald (Thesis advisor) / Mahalov, Alex (Committee member) / Kostelich, Eric (Committee member) / Huang, Huei-Ping (Committee member) / Phelan, Patrick (Committee member) / Arizona State University (Publisher)
Created2013