Matching Items (206)
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
Alkali-activated aluminosilicates, commonly known as "geopolymers", are being increasingly studied as a potential replacement for Portland cement. These binders use an alkaline activator, typically alkali silicates, alkali hydroxides or a combination of both along with a silica-and-alumina rich material, such as fly ash or slag, to form a final product with properties comparable to or better than those of ordinary Portland cement. The kinetics of alkali activation is highly dependent on the chemical composition of the binder material and the activator concentration. The influence of binder composition (slag, fly ash or both), different levels of alkalinity, expressed using the ratios of Na2O-to-binders (n) and activator SiO2-to-Na2O ratios (Ms), on the early age behavior in sodium silicate solution (waterglass) activated fly ash-slag blended systems is discussed in this thesis. Optimal binder composition and the n values are selected based on the setting times. Higher activator alkalinity (n value) is required when the amount of slag in the fly ash-slag blended mixtures is reduced. Isothermal calorimetry is performed to evaluate the early age hydration process and to understand the reaction kinetics of the alkali activated systems. The differences in the calorimetric signatures between waterglass activated slag and fly ash-slag blends facilitate an understanding of the impact of the binder composition on the reaction rates. Kinetic modeling is used to quantify the differences in reaction kinetics using the Exponential as well as the Knudsen method. The influence of temperature on the reaction kinetics of activated slag and fly ash-slag blends based on the hydration parameters are discussed. Very high compressive strengths can be obtained both at early ages as well as later ages (more than 70 MPa) with waterglass activated slag mortars. Compressive strength decreases with the increase in the fly ash content. A qualitative evidence of leaching is presented through the electrical conductivity changes in the saturating solution. The impact of leaching and the strength loss is found to be generally higher for the mixtures made using a higher activator Ms and a higher n value. Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy (ATR-FTIR) is used to obtain information about the reaction products.
ContributorsChithiraputhiran, Sundara Raman (Author) / Neithalath, Narayanan (Thesis advisor) / Rajan, Subramaniyam D (Committee member) / Mobasher, Barzin (Committee member) / Arizona State University (Publisher)
Created2012
Description
Properties of random porous material such as pervious concrete are strongly dependant on its pore structure features. This research deals with the development of an understanding of the relationship between the material structure and the mechanical and functional properties of pervious concretes. The fracture response of pervious concrete specimens proportioned for different porosities, as a function of the pore structure features and fiber volume fraction, is studied. Stereological and morphological methods are used to extract the relevant pore structure features of pervious concretes from planar images. A two-parameter fracture model is used to obtain the fracture toughness (KIC) and critical crack tip opening displacement (CTODc) from load-crack mouth opening displacement (CMOD) data of notched beams under three-point bending. The experimental results show that KIC is primarily dependent on the porosity of pervious concretes. For a similar porosity, an increase in pore size results in a reduction in KIC. At similar pore sizes, the effect of fibers on the post-peak response is more prominent in mixtures with a higher porosity, as shown by the residual load capacity, stress-crack extension relationships, and GR curves. These effects are explained using the mean free spacing of pores and pore-to-pore tortuosity in these systems. A sensitivity analysis is employed to quantify the influence of material design parameters on KIC. This research has also focused on studying the relationship between permeability and tortuosity as it pertains to porosity and pore size of pervious concretes. Various ideal geometric shapes were also constructed that had varying pore sizes and porosities. The pervious concretes also had differing pore sizes and porosities. The permeabilities were determined using three different methods; Stokes solver, Lattice Boltzmann method and the Katz-Thompson equation. These values were then compared to the tortuosity values determined using a Matlab code that uses a pore connectivity algorithm. The tortuosity was also determined from the inverse of the conductivity determined from a numerical analysis that was necessary for using the Katz-Thompson equation. These tortuosity values were then compared to the permeabilities. The pervious concretes and ideal geometric shapes showed consistent similarities betbetween their tortuosities and permeabilities.
ContributorsRehder, Benjamin (Author) / Neithalath, Narayanana (Thesis advisor) / Mobasher, Barzin (Committee member) / Rajan, Subramaniam D. (Committee member) / Arizona State University (Publisher)
Created2013
Description
Buildings consume a large portion of the world's energy, but with the integration of phase change materials (PCMs) in building elements this energy cost can be greatly reduced. The addition of PCMs into building elements, however, becomes a challenge to model and analyze how the material actually affects the energy flow and temperatures in the system. This research work presents a comprehensive computer program used to model and analyze PCM embedded wall systems. The use of the finite element method (FEM) provides the tool to analyze the energy flow of these systems. Finite element analysis (FEA) can model the transient analysis of a typical climate cycle along with nonlinear problems, which the addition of PCM causes. The use of phase change materials is also a costly material expense. The initial expense of using PCMs can be compensated by the reduction in energy costs it can provide. Optimization is the tool used to determine the optimal point between adding PCM into a wall and the amount of energy savings that layer will provide. The integration of these two tools into a computer program allows for models to be efficiently created, analyzed and optimized. The program was then used to understand the benefits between two different wall models, a wall with a single layer of PCM or a wall with two different PCM layers. The effect of the PCMs on the inside wall temperature along with the energy flow across the wall are computed. The numerical results show that a multi-layer PCM wall was more energy efficient and cost effective than the single PCM layer wall. A structural analysis was then performed on the optimized designs using ABAQUS v. 6.10 to ensure the structural integrity of the wall was not affected by adding PCM layer(s).
ContributorsStockwell, Amie (Author) / Rajan, Subramaniam D. (Thesis advisor) / Neithalath, Narayanan (Thesis advisor) / Mobasher, Barzin (Committee member) / Arizona State University (Publisher)
Created2013
Description
Healthy mitochondria are essential for cell survival. Described herein is the synthesis of a family of novel aminoquinone antioxidants designed to alleviate oxidative stress and prevent the impairment of cellular function. In addition, a library of bleomycin disaccharide analogues has also been synthesized to better probe the tumor targeting properties of bleomycin. The first study involves the synthesis of a benzoquinone natural product and analogues that closely resemble the redox core of the natural product geldanamycin. The synthesized 5-amino-3-tridecyl-1,4-benzoquinone antioxidants were tested for their ability to protect Friedreich's ataxia (FRDA) lymphocytes from induced oxidative stress. Some of the analogues synthesized conferred cytoprotection in a dose-dependent manner in FRDA lymphocytes at micromolar concentrations. The biological assays suggest that the modification of the 2-hydroxyl and N-(3-carboxypropyl) groups in the natural product can improve its antioxidant activity and significantly enhance its ability to protect mitochondrial function under conditions of oxidative stress. The second project focused on the synthesis of a library of bleomycin disaccharide-dye conjugates and monitored their cellular uptake by fluorescence microscopy. The studies reveal that the position of the carbamoyl group plays an important role in modulating the cellular uptake of the disaccharide. It also led to the discovery of novel disaccharides with improved tumor selectivity.
ContributorsMathilakathu Madathil, Manikandadas (Author) / Hecht, Sidney M. (Thesis advisor) / Rose, Seth (Committee member) / Woodbury, Neal (Committee member) / Arizona State University (Publisher)
Created2013
Description
ABSTRACT Manipulation of biological targets using synthetic or naturally occurring organic compounds has been the focal point of medicinal chemistry. The work described herein centers on the synthesis of organic small molecules that are targeted either to cell surface receptors, to the ribosomal catalytic center or to human immunodeficiency virus reverse transcriptase. Bleomycins (BLMs) are a family of naturally occurring glycopeptidic antitumor agents with an inherent selectivity towards cancer cells. DeglycoBLM, which lacks the sugar moiety of bleomycin, has much lower cytotoxicity in cellular assays. A recent study using microbbuble conjugates of BLM and deglycoBLM showed that BLM was able to selectively bind to breast cancer cells, whereas the deglyco analogue was unable to target either the cancer or normal cells. This prompted us to further investigate the role of the carbohydrate moiety in bleomycin. Fluorescent conjugates of BLM, deglycoBLM and the BLM carbohydrate were studied for their ability to target cancer cells. Work presented here describes the synthesis of the fluorescent carbohydrate conjugate. Cell culture assays showed that the sugar moiety was able to selectively target various cancer cells. A second conjugate was prepared to study the importance of the C-3 carbamoyl group present on the mannose residue of the carbohydrate. Three additional fluorescent probes were prepared to improve the uptake of this carbohydrate moiety into cancer cells. Encouraged by the results from the fluorescence experiments, the sugar moiety was conjugated to a cytotoxic molecule to selectively deliver this drug into cancer cells. The nonsense codon suppression technique has enabled researchers to site specifically incorporate noncanonical amino acids into proteins. The amino acids successfully incorporated this way are mostly α-L-amino acids. The non-α-L-amino acids are not utilized as substrates by ribosome catalytic center. Hoping that mutations near the ribosome peptidyltransferase site might alleviate its bias towards α-L-amino acids, a library of modified ribosomes was generated. Analogues of the naturally occurring antibiotic puromycin were used to select promising candidates that would allow incorporation of non-α-L-amino acids into proteins. Syntheses of three different puromycin analogues are described here. The reverse transcriptase enzyme from HIV-1 (HIV-1 RT) has been a popular target of HIV therapeutic agents due to its crucial role in viral replication. The 4-chlorophenyl hydrazone of mesoxalic acid (CPHM) was identified in a screen designed to find inhibitors of strand transfer reactions catalyzed by HIV-1 RT. Our collaborators designed several analogues of CPHM with different substituents on the aromatic ring using molecular docking simulations. Work presented here describes the synthesis of eight different analogues of CPHM.
ContributorsPaul, Rakesh (Author) / Hecht, Sidney M. (Thesis advisor) / Moore, Ana L (Committee member) / Rose, Seth D (Committee member) / Arizona State University (Publisher)
Created2013
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
The alkali activation of aluminosilicate materials as binder systems derived from industrial byproducts have been extensively studied due to the advantages they offer in terms enhanced material properties, while increasing sustainability by the reuse of industrial waste and byproducts and reducing the adverse impacts of OPC production. Fly ash and ground granulated blast furnace slag are commonly used for their content of soluble silica and aluminate species that can undergo dissolution, polymerization with the alkali, condensation on particle surfaces and solidification. The following topics are the focus of this thesis: (i) the use of microwave assisted thermal processing, in addition to heat-curing as a means of alkali activation and (ii) the relative effects of alkali cations (K or Na) in the activator (powder activators) on the mechanical properties and chemical structure of these systems. Unsuitable curing conditions instigate carbonation, which in turn lowers the pH of the system causing significant reductions in the rate of fly ash activation and mechanical strength development. This study explores the effects of sealing the samples during the curing process, which effectively traps the free water in the system, and allows for increased aluminosilicate activation. The use of microwave-curing in lieu of thermal-curing is also studied in order to reduce energy consumption and for its ability to provide fast volumetric heating. Potassium-based powder activators dry blended into the slag binder system is shown to be effective in obtaining very high compressive strengths under moist curing conditions (greater than 70 MPa), whereas sodium-based powder activation is much weaker (around 25 MPa). Compressive strength decreases when fly ash is introduced into the system. Isothermal calorimetry is used to evaluate the early hydration process, and to understand the reaction kinetics of the alkali powder activated systems. A qualitative evidence of the alkali-hydroxide concentration of the paste pore solution through the use of electrical conductivity measurements is also presented, with the results indicating the ion concentration of alkali is more prevalent in the pore solution of potassium-based systems. The use of advanced spectroscopic and thermal analysis techniques to distinguish the influence of studied parameters is also discussed.
ContributorsChowdhury, Ussala (Author) / Neithalath, Narayanan (Thesis advisor) / Rajan, Subramanium D. (Committee member) / Mobasher, Barzin (Committee member) / Arizona State University (Publisher)
Created2013
Description
Vector Fitting (VF) is a recent macromodeling method that has been popularized by its use in many commercial software for extracting equivalent circuit's of simulated networks. Specifically for material measurement applications, VF is shown to estimate either the permittivity or permeability of a multi-Debye material accurately, even when measured in the presence of noise and interferences caused by test setup imperfections. A brief history and survey of methods utilizing VF for material measurement will be introduced in this work. It is shown how VF is useful for macromodeling dielectric materials after being measured with standard transmission line and free-space methods. The sources of error in both an admittance tunnel test device and stripline resonant cavity test device are identified and VF is employed for correcting these errors. Full-wave simulations are performed to model the test setup imperfections and the sources of interference they cause are further verified in actual hardware measurements. An accurate macromodel is attained as long as the signal-to-interference-ratio (SIR) in the measurement is sufficiently high such that the Debye relaxations are observable in the data. Finally, VF is applied for macromodeling the time history of the total fields scattering from a perfectly conducting wedge. This effort is an initial test to see if a time domain theory of diffraction exists, and if the diffraction coefficients may be exactly modeled with VF. This section concludes how VF is not only useful for applications in material measurement, but for the solution of modeling fields and interactions in general.
ContributorsRichards, Evan (Author) / Diaz, Rodolfo E (Thesis advisor) / Tsakalis, Konstantinos (Committee member) / Platte, Rodrigo (Committee member) / Arizona State University (Publisher)
Created2013