Matching Items (161)
Description
Deoxyribonucleic acid (DNA), a biopolymer well known for its role in preserving genetic information in biology, is now drawing great deal of interest from material scientists. Ease of synthesis, predictable molecular recognition via Watson-Crick base pairing, vast numbers of available chemical modifications, and intrinsic nanoscale size makes DNA a suitable material for the construction of a plethora of nanostructures that can be used as scaffold to organize functional molecules with nanometer precision. This dissertation focuses on DNA-directed organization of metallic nanoparticles into well-defined, discrete structures and using them to study photonic interaction between fluorophore and metal particle. Presented here are a series of studies toward this goal. First, a novel and robust strategy of DNA functionalized silver nanoparticles (AgNPs) was developed and DNA functionalized AgNPs were employed for the organization of discrete well-defined dimeric and trimeric structures using a DNA triangular origami scaffold. Assembly of 1:1 silver nanoparticle and gold nanoparticle heterodimer has also been demonstrated using the same approach. Next, the triangular origami structures were used to co-assemble gold nanoparticles (AuNPs) and fluorophores to study the distance dependent and nanogap dependencies of the photonic interactions between them. These interactions were found to be consistent with the full electrodynamic simulations. Further, a gold nanorod (AuNR), an anisotropic nanoparticle was assembled into well-defined dimeric structures with predefined inter-rod angles. These dimeric structures exhibited unique optical properties compared to single AuNR that was consistent with the theoretical calculations. Fabrication of otherwise difficult to achieve 1:1 AuNP- AuNR hetero dimer, where the AuNP can be selectively placed at the end-on or side-on positions of anisotropic AuNR has also been shown. Finally, a click chemistry based approach was developed to organize sugar modified DNA on a particular arm of a DNA origami triangle and used them for site-selective immobilization of small AgNPs.
ContributorsPal, Suchetan (Author) / Liu, Yan (Thesis advisor) / Yan, Hao (Thesis advisor) / Lindsay, Stuart (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2012
Description
A signal with time-varying frequency content can often be expressed more clearly using a time-frequency representation (TFR), which maps the signal into a two-dimensional function of time and frequency, similar to musical notation. The thesis reviews one of the most commonly used TFRs, the Wigner distribution (WD), and discusses its application in Fourier optics: it is shown that the WD is analogous to the spectral dispersion that results from a diffraction grating, and time and frequency are similarly analogous to a one dimensional spatial coordinate and wavenumber. The grating is compared with a simple polychromator, which is a bank of optical filters. Another well-known TFR is the short time Fourier transform (STFT). Its discrete version can be shown to be equivalent to a filter bank, an array of bandpass filters that enable localized processing of the analysis signals in different sub-bands. This work proposes a signal-adaptive method of generating TFRs. In order to minimize distortion in analyzing a signal, the method modifies the filter bank to consist of non-overlapping rectangular bandpass filters generated using the Butterworth filter design process. The information contained in the resulting TFR can be used to reconstruct the signal, and perfect reconstruction techniques involving quadrature mirror filter banks are compared with a simple Fourier synthesis sum. The optimal filter parameters of the rectangular filters are selected adaptively by minimizing the mean-squared error (MSE) from a pseudo-reconstructed version of the analysis signal. The reconstruction MSE is proposed as an error metric for characterizing TFRs; a practical measure of the error requires normalization and cross correlation with the analysis signal. Simulations were performed to demonstrate the the effectiveness of the new adaptive TFR and its relation to swept-tuned spectrum analyzers.
ContributorsWeber, Peter C. (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Tepedelenlioğlu, Cihan (Committee member) / Kovvali, Narayan (Committee member) / Arizona State University (Publisher)
Created2012
Description
As the genetic information storage vehicle, deoxyribonucleic acid (DNA) molecules are essential to all known living organisms and many viruses. It is amazing that such a large amount of information about how life develops can be stored in these tiny molecules. Countless scientists, especially some biologists, are trying to decipher the genetic information stored in these captivating molecules. Meanwhile, another group of researchers, nanotechnologists in particular, have discovered that the unique and concise structural features of DNA together with its information coding ability can be utilized for nano-construction efforts. This idea culminated in the birth of the field of DNA nanotechnology which is the main topic of this dissertation. The ability of rationally designed DNA strands to self-assemble into arbitrary nanostructures without external direction is the basis of this field. A series of novel design principles for DNA nanotechnology are presented here, from topological DNA nanostructures to complex and curved DNA nanostructures, from pure DNA nanostructures to hybrid RNA/DNA nanostructures. As one of the most important and pioneering fields in controlling the assembly of materials (both DNA and other materials) at the nanoscale, DNA nanotechnology is developing at a dramatic speed and as more and more construction approaches are invented, exciting advances will emerge in ways that we may or may not predict.
ContributorsHan, Dongran (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Ros, Anexandra (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2012
Description
The ribosome is a ribozyme and central to the biosynthesis of proteins in all organisms. It has a strong bias against non-alpha-L-amino acids, such as alpha-D-amino acids and beta-amino acids. Additionally, the ribosome is only able to incorporate one amino acid in response to one codon. It has been demonstrated that reengineering of the peptidyltransferase center (PTC) of the ribosome enabled the incorporation of both alpha-D-amino acids and beta-amino acids into full length protein. Described in Chapter 2 are five modified ribosomes having modifications in the peptidyltrasnferase center in the 23S rRNA. These modified ribosomes successfully incorporated five different beta-amino acids (2.1 - 2.5) into E. coli dihydrofolate reductase (DHFR). The second project (Chapter 3) focused on the study of the modified ribosomes facilitating the incorporation of the dipeptide glycylphenylalanine (3.25) and fluorescent dipeptidomimetic 3.26 into DHFR. These ribosomes also had modifications in the peptidyltransferase center in the 23S rRNA of the 50S ribosomal subunit. The modified DHFRs having beta-amino acids 2.3 and 2.5, dipeptide glycylphenylalanine (3.25) and dipeptidomimetic 3.26 were successfully characterized by the MALDI-MS analysis of the peptide fragments produced by "in-gel" trypsin digestion of the modified proteins. The fluorescent spectra of the dipeptidomimetic 3.26 and modified DHFR having fluorescent dipeptidomimetic 3.26 were also measured. The type I and II DNA topoisomerases have been firmly established as effective molecular targets for many antitumor drugs. A "classical" topoisomerase I or II poison acts by misaligning the free hydroxyl group of the sugar moiety of DNA and preventing the reverse transesterfication reaction to religate DNA. There have been only two classes of compounds, saintopin and topopyrones, reported as dual topoisomerase I and II poisons. Chapter 4 describes the synthesis and biological evaluation of topopyrones. Compound 4.10, employed at 20 µM, was as efficient as 0.5 uM camptothecin, a potent topoisomerase I poison, in stabilizing the covalent binary complex (~30%). When compared with a known topoisomerase II poison, etoposide (at 0.5 uM), topopyorone 4.10 produced similar levels of stabilized DNA-enzyme binary complex (~34%) at 5 uM concentration.
ContributorsMaini, Rumit (Author) / Hecht, Sidney M. (Thesis advisor) / Gould, Ian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
Distributed inference has applications in a wide range of fields such as source localization, target detection, environment monitoring, and healthcare. In this dissertation, distributed inference schemes which use bounded transmit power are considered. The performance of the proposed schemes are studied for a variety of inference problems. In the first part of the dissertation, a distributed detection scheme where the sensors transmit with constant modulus signals over a Gaussian multiple access channel is considered. The deflection coefficient of the proposed scheme is shown to depend on the characteristic function of the sensing noise, and the error exponent for the system is derived using large deviation theory. Optimization of the deflection coefficient and error exponent are considered with respect to a transmission phase parameter for a variety of sensing noise distributions including impulsive ones. The proposed scheme is also favorably compared with existing amplify-and-forward (AF) and detect-and-forward (DF) schemes. The effect of fading is shown to be detrimental to the detection performance and simulations are provided to corroborate the analytical results. The second part of the dissertation studies a distributed inference scheme which uses bounded transmission functions over a Gaussian multiple access channel. The conditions on the transmission functions under which consistent estimation and reliable detection are possible is characterized. For the distributed estimation problem, an estimation scheme that uses bounded transmission functions is proved to be strongly consistent provided that the variance of the noise samples are bounded and that the transmission function is one-to-one. The proposed estimation scheme is compared with the amplify and forward technique and its robustness to impulsive sensing noise distributions is highlighted. It is also shown that bounded transmissions suffer from inconsistent estimates if the sensing noise variance goes to infinity. For the distributed detection problem, similar results are obtained by studying the deflection coefficient. Simulations corroborate our analytical results. In the third part of this dissertation, the problem of estimating the average of samples distributed at the nodes of a sensor network is considered. A distributed average consensus algorithm in which every sensor transmits with bounded peak power is proposed. In the presence of communication noise, it is shown that the nodes reach consensus asymptotically to a finite random variable whose expectation is the desired sample average of the initial observations with a variance that depends on the step size of the algorithm and the variance of the communication noise. The asymptotic performance is characterized by deriving the asymptotic covariance matrix using results from stochastic approximation theory. It is shown that using bounded transmissions results in slower convergence compared to the linear consensus algorithm based on the Laplacian heuristic. Simulations corroborate our analytical findings. Finally, a robust distributed average consensus algorithm in which every sensor performs a nonlinear processing at the receiver is proposed. It is shown that non-linearity at the receiver nodes makes the algorithm robust to a wide range of channel noise distributions including the impulsive ones. It is shown that the nodes reach consensus asymptotically and similar results are obtained as in the case of transmit non-linearity. Simulations corroborate our analytical findings and highlight the robustness of the proposed algorithm.
ContributorsDasarathan, Sivaraman (Author) / Tepedelenlioğlu, Cihan (Thesis advisor) / Papandreou-Suppappola, Antonia (Committee member) / Reisslein, Martin (Committee member) / Goryll, Michael (Committee member) / Arizona State University (Publisher)
Created2013
Description
The ease of use of mobile devices and tablets by students has generated a lot of interest in the area of engineering education. By using mobile technologies in signal analysis and applied mathematics, undergraduate-level courses can broaden the scope and effectiveness of technical education in classrooms. The current mobile devices have abundant memory and powerful processors, in addition to providing interactive interfaces. Therefore, these devices can support the implementation of non-trivial signal processing algorithms. Several existing visual programming environments such as Java Digital Signal Processing (J-DSP), are built using the platform-independent infrastructure of Java applets. These enable students to perform signal-processing exercises over the Internet. However, some mobile devices do not support Java applets. Furthermore, mobile simulation environments rely heavily on establishing robust Internet connections with a remote server where the processing is performed. The interactive Java Digital Signal Processing tool (iJDSP) has been developed as graphical mobile app on iOS devices (iPads, iPhones and iPod touches). In contrast to existing mobile applications, iJDSP has the ability to execute simulations directly on the mobile devices, and is a completely stand-alone application. In addition to a substantial set of signal processing algorithms, iJDSP has a highly interactive graphical interface where block diagrams can be constructed using a simple drag-n-drop procedure. Functions such as visualization of the convolution operation, and an interface to wireless sensors have been developed. The convolution module animates the process of the continuous and discrete convolution operations, including time-shift and integration, so that users can observe and learn, intuitively. The current set of DSP functions in the application enables students to perform simulation exercises on continuous and discrete convolution, z-transform, filter design and the Fast Fourier Transform (FFT). The interface to wireless sensors in iJDSP allows users to import data from wireless sensor networks, and use the rich suite of functions in iJDSP for data processing. This allows users to perform operations such as localization, activity detection and data fusion. The exercises and the iJDSP application were evaluated by senior-level students at Arizona State University (ASU), and the results of those assessments are analyzed and reported in this thesis.
ContributorsHu, Shuang (Author) / Spanias, Andreas (Thesis advisor) / Tsakalis, Kostas (Committee member) / Tepedelenlioğlu, Cihan (Committee member) / Arizona State University (Publisher)
Created2012
Description
Photovoltaics (PV) is an important and rapidly growing area of research. With the advent of power system monitoring and communication technology collectively known as the "smart grid," an opportunity exists to apply signal processing techniques to monitoring and control of PV arrays. In this paper a monitoring system which provides real-time measurements of each PV module's voltage and current is considered. A fault detection algorithm formulated as a clustering problem and addressed using the robust minimum covariance determinant (MCD) estimator is described; its performance on simulated instances of arc and ground faults is evaluated. The algorithm is found to perform well on many types of faults commonly occurring in PV arrays. Among several types of detection algorithms considered, only the MCD shows high performance on both types of faults.
ContributorsBraun, Henry (Author) / Tepedelenlioğlu, Cihan (Thesis advisor) / Spanias, Andreas (Thesis advisor) / Turaga, Pavan (Committee member) / Arizona State University (Publisher)
Created2012
Description
Deoxyribonucleic acid (DNA) has been treated as excellent building material for nanoscale construction because of its unique structural features. Its ability to self-assemble into predictable and addressable nanostructures distinguishes it from other materials. A large variety of DNA nanostructures have been constructed, providing scaffolds with nanometer precision to organize functional molecules. This dissertation focuses on developing biologically replicating DNA nanostructures to explore their biocompatibility for potential functions in cells, as well as studying the molecular behaviors of DNA origami tiles in higher-order self-assembly for constructing DNA nanostructures with large size and complexity. Presented here are a series of studies towards this goal. First, a single-stranded DNA tetrahedron was constructed and replicated in vivo with high efficiency and fidelity. This study indicated the compatibility between DNA nanostructures and biological systems, and suggested a feasible low-coast method to scale up the preparation of synthetic DNA. Next, the higher-order self-assembly of DNA origami tiles was systematically studied. It was demonstrated that the dimensional aspect ratio of origami tiles as well as the intertile connection design were essential in determining the assembled superstructures. Finally, the effects of DNA hairpin loops on the conformations of origami tiles as well as the higher-order assembled structures were demonstrated. The results would benefit the design and construction of large complex nanostructures.
ContributorsLi, Zhe (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Seo, Dong-Kyun (Committee member) / Wachter, Rebekka (Committee member) / Arizona State University (Publisher)
Created2012
Description
With increased usage of green energy, the number of photovoltaic arrays used in power generation is increasing rapidly. Many of the arrays are located at remote locations where faults that occur within the array often go unnoticed and unattended for large periods of time. Technicians sent to rectify the faults have to spend a large amount of time determining the location of the fault manually. Automated monitoring systems are needed to obtain the information about the performance of the array and detect faults. Such systems must monitor the DC side of the array in addition to the AC side to identify non catastrophic faults. This thesis focuses on two of the requirements for DC side monitoring of an automated PV array monitoring system. The first part of the thesis quantifies the advantages of obtaining higher resolution data from a PV array on detection of faults. Data for the monitoring system can be gathered for the array as a whole or from additional places within the array such as individual modules and end of strings. The fault detection rate and the false positive rates are compared for array level, string level and module level PV data. Monte Carlo simulations are performed using PV array models developed in Simulink and MATLAB for fault and no fault cases. The second part describes a graphical user interface (GUI) that can be used to visualize the PV array for module level monitoring system information. A demonstration GUI is built in MATLAB using data obtained from a PV array test facility in Tempe, AZ. Visualizations are implemented to display information about the array as a whole or individual modules and locate faults in the array.
ContributorsKrishnan, Venkatachalam (Author) / Tepedelenlioğlu, Cihan (Thesis advisor) / Spanias, Andreas (Thesis advisor) / Ayyanar, Raja (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Arizona State University (Publisher)
Created2012
Description
With internet traffic being bursty in nature, Dynamic Bandwidth Allocation(DBA) Algorithms have always been very important for any broadband access network to utilize the available bandwidth effciently. It is no different for Passive Optical Networks(PON), which are networks based on fiber optics in the physical layer of TCP/IP stack or OSI model, which in turn increases the bandwidth in the upper layers. The work in this thesis covers general description of basic DBA Schemes and mathematical derivations that have been established in research. We introduce a Novel Survey Topology that classifes DBA schemes based on their functionality. The novel perspective of classification will be useful in determining which scheme will best suit consumer's needs. We classify DBA as Direct, Intelligent and Predictive back on its computation method and we are able to qualitatively describe their delay and throughput bounds. Also we describe a recently developed DBA Scheme, Multi-thread polling(MTP) used in LRPON and describes the different viewpoints and issues and consequently introduce a novel technique Parallel Polling that overcomes most of issues faced in MTP and that promises better delay performance for LRPON.
ContributorsMercian, Anu (Author) / Reisslein, Martin (Thesis advisor) / McGarry, Michael (Committee member) / Tepedelenlioğlu, Cihan (Committee member) / Zhang, Yanchao (Committee member) / Arizona State University (Publisher)
Created2012