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- All Subjects: engineering
- Creators: Arizona State University
Description
DNA has recently emerged as an extremely promising material to organize molecules on nanoscale. The reliability of base recognition, self-assembling behavior, and attractive structural properties of DNA are of unparalleled value in systems of this size. DNA scaffolds have already been used to organize a variety of molecules including nanoparticles and proteins. New protein-DNA bio-conjugation chemistries make it possible to precisely position proteins and other biomolecules on underlying DNA scaffolds, generating multi-biomolecule pathways with the ability to modulate inter-molecular interactions and the local environment. This dissertation focuses on studying the application of using DNA nanostructure to direct the self-assembly of other biomolecular networks to translate biochemical pathways to non-cellular environments. Presented here are a series of studies toward this application. First, a novel strategy utilized DNA origami as a scaffold to arrange spherical virus capsids into one-dimensional arrays with precise nanoscale positioning. This hierarchical self-assembly allows us to position the virus particles with unprecedented control and allows the future construction of integrated multi-component systems from biological scaffolds using the power of rationally engineered DNA nanostructures. Next, discrete glucose oxidase (GOx)/ horseradish peroxidase (HRP) enzyme pairs were organized on DNA origami tiles with controlled interenzyme spacing and position. This study revealed two different distance-dependent kinetic processes associated with the assembled enzyme pairs. Finally, a tweezer-like DNA nanodevice was designed and constructed to actuate the activity of an enzyme/cofactor pair. Using this approach, several cycles of externally controlled enzyme inhibition and activation were successfully demonstrated. This principle of responsive enzyme nanodevices may be used to regulate other types of enzymes and to introduce feedback or feed-forward control loops.
ContributorsLiu, Minghui (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Zhang, Peiming (Committee member) / Arizona State University (Publisher)
Created2013
Description
The need for a renewable and sustainable light-driven energy source is the motivation for this work, which utilizes a challenging, yet practical and attainable bio-inspired approach to develop an artificial oxygen evolving complex, which builds upon the principles of the natural water splitting mechanism in oxygenic photosynthesis. In this work, a stable framework consisting of a three-dimensional DNA tetrahedron has been used for the design of a bio-mimic of the Oxygen-Evolving Complex (OEC) found in natural Photosystem II (PSII). PSII is a large protein complex that evolves all the oxygen in the atmosphere, but it cannot be used directly in artificial systems, as the light reactions lead to damage of one of Photosystem II's core proteins, D1, which has to be replaced every half hour in the presence of sunlight. The final goal of the project aims to build the catalytic center of the OEC, including the Mn4CaCl metal cluster and its protein environment in the stable DNA framework of a tetrahedron, which can subsequently be connected to a photo-stable artificial reaction center that performs light-induced charge separation. Regions of the peptide sequences containing Mn4CaCl ligation sites are implemented in the design of the aOEC (artificial oxygen-evolving complex) and are attached to sites within the tetrahedron to facilitate assembly. Crystals of the tetrahedron have been obtained, and X-ray crystallography has been used for characterization. As a proof of concept, metal-binding peptides have been coupled to the DNA tetrahedron which allowed metal-containing porphyrins, specifically Fe(III) meso-Tetra(4-sulfonatophenyl) porphyrin chloride, to be encapsulated inside the DNA-tetrahedron. The porphyrins were successfully assembled inside the tetrahedron through coordination of two terminal histidines from the orthogonally oriented peptides covalently attached to the DNA. The assembly has been characterized using Electron Paramagnetic Resonance (EPR), optical spectroscopy, Dynamic Light Scattering (DLS), and x-ray crystallography. The results reveal that the spin state of the metal, iron (III), switches during assembly from the high-spin state to low-spin state.
ContributorsRendek, Kimberly Nicole (Author) / Fromme, Petra (Thesis advisor) / Chen, Julian (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2012
Description
The F1Fo ATP synthase is required for energy conversion in almost all living organisms. The F1 complex is a molecular motor that uses ATP hydrolysis to drive rotation of the γ–subunit. It has not been previously possible to resolve the speed and position of the γ–subunit of the F1–ATPase as it rotates during a power stroke. The single molecule experiments presented here measured light scattered from 45X91 nm gold nanorods attached to the γ–subunit that provide an unprecedented 5 μs resolution of rotational position as a function of time. The product of velocity and drag, which were both measured directly, resulted in an average torque of 63±8 pN nm for the Escherichia coli F1-ATPase that was determined to be independent of the load. The rotational velocity had an initial (I) acceleration phase 15° from the end of the catalytic dwell, a slow (S) acceleration phase during ATP binding/ADP release (15°–60°), and a fast (F) acceleration phase (60°–90°) containing an interim deceleration (ID) phase (75°–82°). High ADP concentrations decreased the velocity of the S phase proportional to 'ADP-release' dwells, and the F phase proportional to the free energy derived from the [ADP][Pi]/[ATP] chemical equilibrium. The decreased affinity for ITP increased ITP-binding dwells by 10%, but decreased velocity by 40% during the S phase. This is the first direct evidence that nucleotide binding contributes to F1–ATPase torque. Mutations that affect specific phases of rotation were identified, some in regions of F1 previously considered not to contribute to rotation. Mutations βD372V and γK9I increased the F phase velocity, and γK9I increased the depth of the ID phase. The conversion between S and F phases was specifically affected by γQ269L. While βT273D, βD305E, and αR283Q decreased the velocity of all phases, decreases in velocity due to βD302T, γR268L and γT82A were confined to the I and S phases. The correlations between the structural locations of these mutations and the phases of rotation they affect provide new insight into the molecular basis for F1–ATPase γ-subunit rotation.
ContributorsMartin, James (Author) / Frasch, Wayne D (Thesis advisor) / Chandler, Douglas (Committee member) / Gaxiola, Roberto (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2012
Description
The use of electromyography (EMG) signals to characterize muscle fatigue has been widely accepted. Initial work on characterizing muscle fatigue during isometric contractions demonstrated that its frequency decreases while its amplitude increases with the onset of fatigue. More recent work concentrated on developing techniques to characterize dynamic contractions for use in clinical and training applications. Studies demonstrated that as fatigue progresses, the EMG signal undergoes a shift in frequency, and different physiological mechanisms on the possible cause of the shift were considered. Time-frequency processing, using the Wigner distribution or spectrogram, is one of the techniques used to estimate the instantaneous mean frequency and instantaneous median frequency of the EMG signal using a variety of techniques. However, these time-frequency methods suffer either from cross-term interference when processing signals with multiple components or time-frequency resolution due to the use of windowing. This study proposes the use of the matching pursuit decomposition (MPD) with a Gaussian dictionary to process EMG signals produced during both isometric and dynamic contractions. In particular, the MPD obtains unique time-frequency features that represent the EMG signal time-frequency dependence without suffering from cross-terms or loss in time-frequency resolution. As the MPD does not depend on an analysis window like the spectrogram, it is more robust in applying the timefrequency features to identify the spectral time-variation of the EGM signal.
ContributorsAustin, Hiroko (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Kovvali, Narayan (Committee member) / Muthuswamy, Jitendran (Committee member) / Arizona State University (Publisher)
Created2012
Description
An issue with the utilization of swimming pools is that pumps are operated an excessive number of hours to keep the pool free of debris and algae. Case in point, according to the pool industry, a pump should operate one hour for every ten degrees of ambient temperature. A dynamic model and a control strategy have been developed using Matlab/Simulink that uses environmental conditions together with chemicals that hinder or aid algae growth in order to determine algae population. This model suggests ways to function the pump on shorter time intervals to reduce energy consumption, while simultaneously maintaining algae populations at acceptable levels. Other factors included in the model are pool thermal dynamics and pool pump/filter performance characteristics, since they also have an effect algae growth. This thesis presents the first step for an alternative way of operating a swimming pool by minimizing operating costs while eliminating algae.
ContributorsBallard, Roderick (Author) / Macia, Narciso (Thesis advisor) / Narveson, Brentt (Committee member) / Mchenry, Albert (Committee member) / Dempster, Thomas (Committee member) / Arizona State University (Publisher)
Created2012
Description
Ball Grid Array (BGA) using lead-free or lead-rich solder materials are widely used as Second Level Interconnects (SLI) in mounting packaged components to the printed circuit board (PCB). The reliability of these solder joints is of significant importance to the performance of microelectronics components and systems. Product design/form-factor, solder material, manufacturing process, use condition, as well as, the inherent variabilities present in the system, greatly influence product reliability. Accurate reliability analysis requires an integrated approach to concurrently account for all these factors and their synergistic effects. Such an integrated and robust methodology can be used in design and development of new and advanced microelectronics systems and can provide significant improvement in cycle-time, cost, and reliability. IMPRPK approach is based on a probabilistic methodology, focusing on three major tasks of (1) Characterization of BGA solder joints to identify failure mechanisms and obtain statistical data, (2) Finite Element analysis (FEM) to predict system response needed for life prediction, and (3) development of a probabilistic methodology to predict the reliability, as well as, the sensitivity of the system to various parameters and the variabilities. These tasks and the predictive capabilities of IMPRPK in microelectronic reliability analysis are discussed.
ContributorsFallah-Adl, Ali (Author) / Tasooji, Amaneh (Thesis advisor) / Krause, Stephen (Committee member) / Alford, Terry (Committee member) / Jiang, Hanqing (Committee member) / Mahajan, Ravi (Committee member) / Arizona State University (Publisher)
Created2013
Description
While the piezoelectric effect has been around for some time, it has only recently caught interest as a potential sustainable energy harvesting device. Piezoelectric energy harvesting has been developed for shoes and panels, but has yet to be integrated into a marketable bicycle tire. For this thesis, the development and feasibility of a piezoelectric tire was done. This includes the development of a circuit that incorporates piezoceramic elements, energy harvesting circuitry, and an energy storage device. A single phase circuit was designed using an ac-dc diode rectifier. An electrolytic capacitor was used as the energy storage device. A financial feasibility was also done to determine targets for manufacturing cost and sales price. These models take into account market trends for high performance tires, economies of scale, and the possibility of government subsidies. This research will help understand the potential for the marketability of a piezoelectric energy harvesting tire that can create electricity for remote use. This study found that there are many obstacles that must be addressed before a piezoelectric tire can be marketed to the general public. The power output of this device is miniscule compared to an alkaline battery. In order for this device to approach the power output of an alkaline battery the weight of the device would also become an issue. Additionally this device is very costly compared to the average bicycle tire. Lastly, this device is extreme fragile and easily broken. In order for this device to become marketable the issues of power output, cost, weight, and durability must all be successfully overcome.
ContributorsMalotte, Christopher (Author) / Madakannan, Arunachalanadar (Thesis advisor) / Srinivasan, Devarajan (Committee member) / Rogers, Bradley (Committee member) / Arizona State University (Publisher)
Created2012
Description
Microgrids are a subset of the modern power structure; using distributed generation (DG) to supply power to communities rather than vast regions. The reduced scale mitigates loss allowing the power produced to do more with better control, giving greater security, reliability, and design flexibility. This paper explores the performance and cost viability of a hybrid grid-tied microgrid that utilizes Photovoltaic (PV), batteries, and fuel cell (FC) technology. The concept proposes that each community home is equipped with more PV than is required for normal operation. As the homes are part of a microgrid, excess or unused energy from one home is collected for use elsewhere within the microgrid footprint. The surplus power that would have been discarded becomes a community asset, and is used to run intermittent services. In this paper, the modeled community does not have parking adjacent to each home allowing for the installment of a privately owned slower Level 2 charger, making EV ownership option untenable. A solution is to provide a Level 3 DC Quick Charger (DCQC) as the intermittent service. The addition of batteries and Fuel Cells are meant to increase load leveling, reliability, and instill limited island capability.
ContributorsPatterson, Maxx (Author) / Madakannan, Arunachalanadar (Thesis advisor) / Macia, Narciso (Committee member) / Peng, Xihong (Committee member) / Arizona State University (Publisher)
Created2013
Description
The Solid State Transformer (SST) is an essential component in the FREEDM system. This research focuses on the modeling of the SST and the controller hardware in the loop (CHIL) implementation of the SST for the support of the FREEDM system demonstration. The energy based control strategy for a three-stage SST is analyzed and applied. A simplified average model of the three-stage SST that is suitable for simulation in real time digital simulator (RTDS) has been developed in this study. The model is also useful for general time-domain power system analysis and simulation. The proposed simplified av-erage model has been validated in MATLAB and PLECS. The accuracy of the model has been verified through comparison with the cycle-by-cycle average (CCA) model and de-tailed switching model. These models are also implemented in PSCAD, and a special strategy to implement the phase shift modulation has been proposed to enable the switching model simulation in PSCAD. The implementation of the CHIL test environment of the SST in RTDS is described in this report. The parameter setup of the model has been discussed in detail. One of the dif-ficulties is the choice of the damping factor, which is revealed in this paper. Also the grounding of the system has large impact on the RTDS simulation. Another problem is that the performance of the system is highly dependent on the switch parameters such as voltage and current ratings. Finally, the functionalities of the SST have been realized on the platform. The distributed energy storage interface power injection and reverse power flow have been validated. Some limitations are noticed and discussed through the simulation on RTDS.
ContributorsJiang, Youyuan (Author) / Ayyanar, Raja (Thesis advisor) / Holbert, Keith E. (Committee member) / Chowdhury, Srabanti (Committee member) / Arizona State University (Publisher)
Created2014
Description
Humans are capable of transferring learning for anticipatory control of dexterous object manipulation despite changes in degrees-of-freedom (DoF), i.e., switching from lifting an object with two fingers to lifting the same object with three fingers. However, the role that tactile information plays in this transfer of learning is unknown. In this study, subjects lifted an L-shaped object with two fingers (2-DoF), and then lifted the object with three fingers (3-DoF). The subjects were divided into two groups--one group performed the task wearing a glove (to reduce tactile sensibility) upon the switch to 3-DoF (glove group), while the other group did not wear the glove (control group). Compensatory moment (torque) was used as a measure to determine how well the subject could minimize the tilt of the object following the switch from 2-DoF to 3-DoF. Upon the switch to 3-DoF, subjects wearing the glove generated a compensatory moment (Mcom) that had a significantly higher error than the average of the last five trials at the end of the 3-DoF block (p = 0.012), while the control subjects did not demonstrate a significant difference in Mcom. Additional effects of the reduction in tactile sensibility were: (1) the grip force for the group of subjects wearing the glove was significantly higher in the 3-DoF trials compared to the 2-DoF trials (p = 0.014), while the grip force of the control subjects was not significantly different; (2) the difference in centers of pressure between the thumb and fingers (ΔCoP) significantly increased in the 3-DoF block for the group of subjects wearing the glove, while the ΔCoP of the control subjects was not significantly different; (3) lastly, the control subjects demonstrated a greater increase in lift force than the group of subjects wearing the glove (though results were not significant). Combined together, these results suggest different force modulation strategies are used depending on the amount of tactile feedback that is available to the subject. Therefore, reduction of tactile sensibility has important effects on subjects' ability to transfer learned manipulation across different DoF contexts.
ContributorsGaw, Nathan (Author) / Helms Tillery, Stephen (Thesis advisor) / Santello, Marco (Committee member) / Kleim, Jeffrey (Committee member) / Arizona State University (Publisher)
Created2014