Matching Items (215)
Description
DNA nanotechnology has been a rapidly growing research field in the recent decades, and there have been extensive efforts to construct various types of highly programmable and robust DNA nanostructures. Due to the advantage that DNA nanostructure can be used to organize biochemical molecules with precisely controlled spatial resolution, herein we used DNA nanostructure as a scaffold for biological applications. Targeted cell-cell interaction was reconstituted through a DNA scaffolded multivalent bispecific aptamer, which may lead to promising potentials in tumor therapeutics. In addition a synthetic vaccine was constructed using DNA nanostructure as a platform to assemble both model antigen and immunoadjuvant together, and strong antibody response was demonstrated in vivo, highlighting the potential of DNA nanostructures to serve as a new platform for vaccine construction, and therefore a DNA scaffolded hapten vaccine is further constructed and tested for its antibody response. Taken together, my research demonstrated the potential of DNA nanostructure to serve as a general platform for immunological applications.
ContributorsLiu, Xiaowei (Author) / Liu, Yan (Thesis advisor) / Chang, Yung (Thesis advisor) / Yan, Hao (Committee member) / Allen, James (Committee member) / Zhang, Peiming (Committee member) / Arizona State University (Publisher)
Created2012
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
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
Laboratory assessment of crack resistance and propagation in asphalt concrete is a difficult task that challenges researchers and engineers. Several fracture mechanics based laboratory tests currently exist; however, these tests and subsequent analysis methods rely on elastic behavior assumptions and do not consider the time-dependent nature of asphalt concrete. The C* Line Integral test has shown promise to capture crack resistance and propagation within asphalt concrete. In addition, the fracture mechanics based C* parameter considers the time-dependent creep behavior of the materials. However, previous research was limited and lacked standardized test procedure and detailed data analysis methods were not fully presented. This dissertation describes the development and refinement of the C* Fracture Test (CFT) based on concepts of the C* line integral test. The CFT is a promising test to assess crack propagation and fracture resistance especially in modified mixtures. A detailed CFT test protocol was developed based on a laboratory study of different specimen sizes and test conditions. CFT numerical simulations agreed with laboratory results and indicated that the maximum horizontal tensile stress (Mode I) occurs at the crack tip but diminishes at longer crack lengths when shear stress (Mode II) becomes present. Using CFT test results and the principles of time-temperature superposition, a crack growth rate master curve was successfully developed to describe crack growth over a range of test temperatures. This master curve can be applied to pavement design and analysis to describe crack propagation as a function of traffic conditions and pavement temperatures. Several plant mixtures were subjected to the CFT and results showed differences in resistance to crack propagation, especially when comparing an asphalt rubber mixture to a conventional one. Results indicated that crack propagation is ideally captured within a given range of dynamic modulus values. Crack growth rates and C* prediction models were successfully developed for all unmodified mixtures in the CFT database. These models can be used to predict creep crack propagation and the C* parameter when laboratory testing is not feasible. Finally, a conceptual approach to incorporate crack growth rate and the C* parameter into pavement design and analysis was presented.
ContributorsStempihar, Jeffrey (Author) / Kaloush, Kamil (Thesis advisor) / Witczak, Matthew (Committee member) / Mamlouk, Michael (Committee member) / Arizona State University (Publisher)
Created2013
Description
One of the main requirements of designing perpetual pavements is to determine the endurance limit of Hot Mix Asphalt (HMA). The purpose of this study was to validate the endurance limit for HMA using laboratory beam fatigue tests. A mathematical procedure was developed to determine the endurance limit of HMA due to healing that occurs during the rest periods between loading cycles. Relating healing to endurance limit makes this procedure unique compared to previous research projects that investigated these concepts separately. An extensive laboratory testing program, including 468 beam tests, was conducted according to AASHTO T321-03 test procedure. Six factors that affect the fatigue response of HMA were evaluated: binder type, binder content, air voids, test temperature, rest period and applied strain. The endurance limit was determined when no accumulated damage occurred indicating complete healing. Based on the test results, a first generation predictive model was developed to relate stiffness ratio to material properties. A second generation stiffness ratio model was also developed by replacing four factors (binder type, binder content, air voids, and temperature) with the initial stiffness of the mixture, which is a basic material property. The model also accounts for the nonlinear effects of the rest period and the applied strain on the healing and endurance limit. A third generation model was then developed by incorporation the number of loading cycles at different locations along the fatigue degradation curve for each test in order to account for the nonlinearity between stiffness ratio and loading cycles. In addition to predicting endurance limit, the model has the ability to predict the number of cycles to failure at any rest period and stiffness combination. The model was used to predict fatigue relationship curves for tests with rest period and determining the K1, K2, and K3 fatigue cracking coefficients. The three generation models predicted close endurance limit values ranging from 22 to 204 micro strains. After developing the third generation stiffness ratio model, the predicted endurance limit values were integrated in the strain-Nf fatigue relationships as a step toward incorporating the endurance limit in the MEPDG software. The results of this study can be used to design perpetual pavements that can sustain a large number of loads if traffic volumes and vehicle weights are controlled.
ContributorsSouliman, Mena (Author) / Mamlouk, Michael S. (Thesis advisor) / Witczak, Matthew W. (Thesis advisor) / Kaloush, Kamil (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
The application of fibers and other materials in asphalt mixes has been studied and applied over the past five decades in order to improve pavement performance around the world. This thesis highlights the characteristics and performance properties of modified asphalt mixes using a blend of polypropylene and aramid fibers, The main objective of this study was to evaluate the effect of adding different fiber dosages on the laboratory performance of both asphalt binder and mixture. The laboratory study was conducted on sixteen different dosages and blends of the fibers, with various combinations of polypropylene and aramid, using binder tests as well as hot mix asphalt tests. The binder tests included: penetration, softing point, and Brookfield viscosity tests. The asphalt mixture tests included the dynamic modulus, and indirect tensile strength. The binder test results indicated that the best viscosity - temperature susceptibility performance would be from the blend of three dosages of polypropylene and one dosage of aramid, the dynamic modulus test results also confirmed this finding. Overall, in almost every case, the addition of fibers resulted in an increase in mixture stiffness regardless of fiber content. From the indirect tensile strength results, the polypropylene fibers had less of an effect on post peak failure than the aramid fibers. Overall, the aramid fibers yielded better results than the polypropylene fibers. This study has important implications for the future of pavement design and the prospect of using optimal dosages of polypropylene and aramid fibers in further research to further determine their long-term performance and characteristics used in real world applications.
ContributorsAlrajhi, Ashraf (Author) / Kaloush, Kamil (Thesis advisor) / Mamlouk, Michael (Committee member) / Witzcak, Matthew (Committee member) / Arizona State University (Publisher)
Created2012
Description
The development of microsimulation approaches to urban systems modeling has occurred largely in three parallel streams of research, namely, land use, travel demand and traffic assignment. However, there are important dependencies and inter-relationships between the model systems which need to be accounted to accurately and comprehensively model the urban system. Location choices affect household activity-travel behavior, household activity-travel behavior affects network level of service (performance), and network level of service, in turn, affects land use and activity-travel behavior. The development of conceptual designs and operational frameworks that represent such complex inter-relationships in a consistent fashion across behavioral units, geographical entities, and temporal scales has proven to be a formidable challenge. In this research, an integrated microsimulation modeling framework called SimTRAVEL (Simulator of Transport, Routes, Activities, Vehicles, Emissions, and Land) that integrates the component model systems in a behaviorally consistent fashion, is presented. The model system is designed such that the activity-travel behavior model and the dynamic traffic assignment model are able to communicate with one another along continuous time with a view to simulate emergent activity-travel patterns in response to dynamically changing network conditions. The dissertation describes the operational framework, presents the modeling methodologies, and offers an extensive discussion on the advantages that such a framework may provide for analyzing the impacts of severe network disruptions on activity-travel choices. A prototype of the model system is developed and implemented for a portion of the Greater Phoenix metropolitan area in Arizona to demonstrate the capabilities of the model system.
ContributorsKonduri, Karthik Charan (Author) / Pendyala, Ram M. (Thesis advisor) / Ahn, Soyoung (Committee member) / Kuby, Michael (Committee member) / Kaloush, Kamil (Committee member) / Arizona State University (Publisher)
Created2012
Description
The current method of measuring thermal conductivity requires flat plates. For most common civil engineering materials, creating or extracting such samples is difficult. A prototype thermal conductivity experiment had been developed at Arizona State University (ASU) to test cylindrical specimens but proved difficult for repeated testing. In this study, enhancements to both testing methods were made. Additionally, test results of cylindrical testing were correlated with the results from identical materials tested by the Guarded Hot&ndashPlate; method, which uses flat plate specimens. In validating the enhancements made to the Guarded Hot&ndashPlate; and Cylindrical Specimen methods, 23 tests were ran on five different materials. The percent difference shown for the Guarded Hot&ndashPlate; method was less than 1%. This gives strong evidence that the enhanced Guarded Hot-Plate apparatus in itself is now more accurate for measuring thermal conductivity. The correlation between the thermal conductivity values of the Guarded Hot&ndashPlate; to those of the enhanced Cylindrical Specimen method was excellent. The conventional concrete mixture, due to much higher thermal conductivity values compared to the other mixtures, yielded a P&ndashvalue; of 0.600 which provided confidence in the performance of the enhanced Cylindrical Specimen Apparatus. Several recommendations were made for the future implementation of both test methods. The work in this study fulfills the research community and industry desire for a more streamlined, cost effective, and inexpensive means to determine the thermal conductivity of various civil engineering materials.
ContributorsMorris, Derek (Author) / Kaloush, Kamil (Thesis advisor) / Mobasher, Barzin (Committee member) / Phelan, Patrick E (Committee member) / Arizona State University (Publisher)
Created2011