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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
Wide spread adoption of photovoltaic technology is limited by cost. Developing photovoltaics based on low-cost materials and processing techniques is one strategy for reducing the cost of electricity generated by photovoltaics. With this in mind, novel porphyrin and porphyrin-fullerene electropolymers have been developed here at Arizona State University. Porphyrins are attractive for inclusion in the light absorbing layer of photovoltaics due to their high absorption coefficients (on the order of 105 cm-1) and porphyrin-fullerene dyads are attractive for use in photovoltaics due to their ability to produce ultrafast photoinduced charge separation (on the order of 10-15 s). The focus of this thesis is the characterization of the photovoltaic properties of these electropolymer films. Films formed on transparent conductive oxide (TCO) substrates were contacted using a mercury drop electrode in order to measure photocurrent spectra and current-voltage curves. Surface treatment of both the TCO substrate and the mercury drop is shown to have a dramatic effect on the photovoltaic performance of the electropolymer films. Treating the TCO substrates with chlorotrimethylsilane and the mercury drop with hexanethiol was found to produce an optimal tradeoff between photocurrent and photovoltage. Incident photon to current efficiency spectra of the films show that the dominant photocurrent generation mechanism in this system is located at the polymer-mercury interface. The optical field intensity at this interface approaches zero due to interference from the light reflected by the mercury surface. Reliance upon photocurrent generation at this interface limits the performance of this system and suggests that these polymers may be useful in solar cells which have structures optimized to take advantage of their internal optical field distributions.
ContributorsBridgewater, James W (Author) / Gust, Devens (Thesis advisor) / Tao, Nongjian (Thesis advisor) / Gould, Ian (Committee member) / Diaz, Rodolfo (Committee member) / Arizona State University (Publisher)
Created2014
Description
DNA is a unique, highly programmable and addressable biomolecule. Due to its reliable and predictable base recognition behavior, uniform structural properties, and extraordinary stability, DNA molecules are desirable substrates for biological computation and nanotechnology. The field of DNA computation has gained considerable attention due to the possibility of exploiting the massive parallelism that is inherent in natural systems to solve computational problems. This dissertation focuses on building novel types of computational DNA systems based on both DNA reaction networks and DNA nanotechnology. A series of related research projects are presented here. First, a novel, three-input majority logic gate based on DNA strand displacement reactions was constructed. Here, the three inputs in the majority gate have equal priority, and the output will be true if any two of the inputs are true. We subsequently designed and realized a complex, 5-input majority logic gate. By controlling two of the five inputs, the complex gate is capable of realizing every combination of OR and AND gates of the other 3 inputs. Next, we constructed a half adder, which is a basic arithmetic unit, from DNA strand operated XOR and AND gates. The aim of these two projects was to develop novel types of DNA logic gates to enrich the DNA computation toolbox, and to examine plausible ways to implement large scale DNA logic circuits. The third project utilized a two dimensional DNA origami frame shaped structure with a hollow interior where DNA hybridization seeds were selectively positioned to control the assembly of small DNA tile building blocks. The small DNA tiles were directed to fill the hollow interior of the DNA origami frame, guided through sticky end interactions at prescribed positions. This research shed light on the fundamental behavior of DNA based self-assembling systems, and provided the information necessary to build programmed nanodisplays based on the self-assembly of DNA.
ContributorsLi, Wei (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Colloidal quantum dots (QDs) or semiconductor nanocrystals are often used to describe 2 to 20 nm solution processed nanoparticles of various semiconductor materials that display quantum confinement effects. Compared to traditional fluorescent organic dyes, QDs provide many advantages. For biological applications it is necessary to develop reliable methods to functionalize QDs with hydrophilic biomolecules so that they may maintain their stability and functionality in physiological conditions. DNA, a molecule that encodes genetic information, is arguably the smartest molecule that nature has ever produced and one of the most explored bio-macromolecules. DNA directed self-assembly can potentially organize QDs that are functionalized with DNA with nanometer precision, and the resulting arrangements may facilitate the display of novel optical properties. The goal of this dissertation was to achieve a robust reliable yet simple strategy to link DNA to QDs so that they can be used for DNA directed self assembly by which we can engineer their optical properties. Presented here is a series of studies to achieve this goal. First we demonstrate the aqueous synthesis of colloidal nanocrystal heterostructures consisting of the CdTe core encapsulated by CdS/ZnS or CdSe/ZnS shells using glutathione (GSH), a tripeptide, as the capping ligand. We next employed this shell synthesis strategy to conjugate PS-PO chimeric DNA to QDs at the time of shell synthesis. We synthesized a library of DNA linked QDs emitting from UV to near IR that are very stable in high salt concentrations. These DNA functionalized QDs were further site-specifically organized on DNA origami in desired patterns directed by DNA self-assembly. We further extended our capability to functionalize DNA to real IR emitting CdxPb1-xTe alloyed QDs, and demonstrated their stability by self-assembling them on DNA origami. The photo-physical properties of the QDs were further engineered by attaching a QD and a gold nanoparticle in controlled distances on the same DNA origami, which revealed a much longer range quenching effect than usual Forster Resonance Energy Transfer. We are currently engaged in enhancing photoluminescence intensity of the QDs by bringing them in the plasmonic hot spots generated by cluster of larger plasmonic nanoparticles.
ContributorsSamanta, Anirban (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Buttry, Daniel (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Nanolasers represents the research frontier in both the areas of photonics and nanotechnology for its interesting properties in low dimension physics, its appealing prospects in integrated photonics, and other on-chip applications. In this thesis, I present my research work on fabrication and characterization of a new type of nanolasers: metallic cavity nanolasers. The last ten years witnessed a dramatic paradigm shift from pure dielectric cavity to metallic cavity in the research of nanolasers. By using low loss metals such as silver, which is highly reflective at near infrared, light can be confined in an ultra small cavity or waveguide with sub-wavelength dimensions, thus enabling sub-wavelength cavity lasers. Based on this idea, I fabricated two different kinds of metallic cavity nanolasers with rectangular and circular geometries with InGaAs as the gain material and silver as the metallic shell. The lasing wavelength is around 1.55 μm, intended for optical communication applications. Continuous wave (CW) lasing at cryogenic temperature under current injection was achieved on devices with a deep sub-wavelength physical cavity volume smaller than 0.2 λ3. Improving device fabrication process is one of the main challenges in the development of metallic cavity nanolasers due to its ultra-small size. With improved fabrication process and device design, CW lasing at room temperature was demonstrated as well on a sub-wavelength rectangular device with a physical cavity volume of 0.67 λ3. Experiments verified that a small circular nanolasers supporting TE¬01 mode can generate an azimuthal polarized laser beam, providing a compact such source under electrical injection. Sources with such polarizations could have many special applications. Study of digital modulation of circular nanolasers showed that laser noise is an important factor that will affect the data rate of the nanolaser when used as the light source in optical interconnects. For future development, improving device fabrication processes is required to improve device performance. In addition, techniques need to be developed to realize nanolaser/Si waveguide integration. In essence, resolving these two critical issues will finally pave the way for these nanolasers to be used in various practical applications.
ContributorsDing, Kang (Author) / Ning, Cun-Zheng (Thesis advisor) / Yu, Hongbin (Committee member) / Palais, Joseph (Committee member) / Zhang, Yong-Hang (Committee member) / Arizona State University (Publisher)
Created2014
Description
DNA nanotechnology is one of the most flourishing interdisciplinary research fields. Through the features of programmability and predictability, DNA nanostructures can be designed to self-assemble into a variety of periodic or aperiodic patterns of different shapes and length scales, and more importantly, they can be used as scaffolds for organizing other nanoparticles, proteins and chemical groups. By leveraging these molecules, DNA nanostructures can be used to direct the organization of complex bio-inspired materials that may serve as smart drug delivery systems and in vitro or in vivo bio-molecular computing and diagnostic devices. In this dissertation I describe a systematic study of the thermodynamic properties of complex DNA nanostructures, including 2D and 3D DNA origami, in order to understand their assembly, stability and functionality and inform future design endeavors. It is conceivable that a more thorough understanding of DNA self-assembly can be used to guide the structural design process and optimize the conditions for assembly, manipulation, and functionalization, thus benefiting both upstream design and downstream applications. As a biocompatible nanoscale motif, the successful integration, stabilization and separation of DNA nanostructures from cells/cell lysate suggests its potential to serve as a diagnostic platform at the cellular level. Here, DNA origami was used to capture and identify multiple T cell receptor mRNA species from single cells within a mixed cell population. This demonstrates the potential of DNA nanostructure as an ideal nano scale tool for biological applications.
ContributorsWei, Xixi (Author) / Liu, Yan (Thesis advisor) / Yan, Hao (Thesis advisor) / Chen, Julian (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Multiple quantum well (MQW) structures have been employed in a variety of solid state devices. The InGaAs/GaAs material system is of special interest for many optoelectronic applications. This study examines epitaxial growth and defect creation in InGaAs/GaAs MQWs at its initial stage. Correlations between physical properties, crystal perfection of epitaxial structures, and growth conditions under which desired properties are achieved appear as highly important for the realization and final performance of semiconductor based devices.
Molecular beam epitaxy was utilized to grow InGaAs/GaAs MQW structures with a variation in deposition temperature Tdep among the samples to change crystalline and physical properties. High resolution x-ray diffraction and transmission electron microscopy were utilized to probe crystal properties, whereas photoluminescence spectroscopy evaluated optical response. An optimal growth temperature Tdep=505°C was found for 20% In composition. The density of 60° primary and secondary dislocation loops increased continuously at lower growth temperatures and reduced crystal perfection, as evaluated by lateral and vertical coherence lengths and diffuse scattering in reciprocal space maps. Likewise, the strength of non-radiative Shockley-Read-Hall recombination increased as deposition temperature was reduced. Elevated deposition temperature led to InGaAs decay in the structures and manifested in different crystalline defects with a rather isotropic distribution and no lateral ordering. High available thermal energy increased atomic surface diffusivity and resulted in growth surface instability against perturbations, manifesting in lateral layer thickness undulations. Carriers in structures grown at elevated temperature experience localization in local energy minima.InGaAs/GaAs MQW structures reveal correlation between their crystal quality and optical properties. It can be suggested that there is an optimal growth temperature range for each In composition with high crystal perfection and best physical response.
Molecular beam epitaxy was utilized to grow InGaAs/GaAs MQW structures with a variation in deposition temperature Tdep among the samples to change crystalline and physical properties. High resolution x-ray diffraction and transmission electron microscopy were utilized to probe crystal properties, whereas photoluminescence spectroscopy evaluated optical response. An optimal growth temperature Tdep=505°C was found for 20% In composition. The density of 60° primary and secondary dislocation loops increased continuously at lower growth temperatures and reduced crystal perfection, as evaluated by lateral and vertical coherence lengths and diffuse scattering in reciprocal space maps. Likewise, the strength of non-radiative Shockley-Read-Hall recombination increased as deposition temperature was reduced. Elevated deposition temperature led to InGaAs decay in the structures and manifested in different crystalline defects with a rather isotropic distribution and no lateral ordering. High available thermal energy increased atomic surface diffusivity and resulted in growth surface instability against perturbations, manifesting in lateral layer thickness undulations. Carriers in structures grown at elevated temperature experience localization in local energy minima.InGaAs/GaAs MQW structures reveal correlation between their crystal quality and optical properties. It can be suggested that there is an optimal growth temperature range for each In composition with high crystal perfection and best physical response.
ContributorsKarow, Matthias (Author) / Honsberg, C. (Christiana B.) (Thesis advisor) / Faleev, Nikolai N (Committee member) / Ning, Cun-Zheng (Committee member) / Arizona State University (Publisher)
Created2014
Description
This dissertation aims to demonstrate a new approach to fabricating solar cells for spectrum-splitting photovoltaic systems with the potential to reduce their cost and complexity of manufacturing, called Monolithically Integrated Laterally Arrayed Multiple Band gap (MILAMB) solar cells. Single crystal semiconductor alloy nanowire (NW) ensembles are grown with the alloy composition and band gap changing continuously across a broad range over the surface of a single substrate in a single, inexpensive growth step by the Dual-Gradient Method. The nanowire ensembles then serve as the absorbing materials in a set of solar cells for spectrum-splitting photovoltaic systems.
Preliminary design and simulation studies based on Anderson's model band line-ups were undertaken for CdPbS and InGaN alloys. Systems of six subcells obtained efficiencies in the 32-38% range for CdPbS and 34-40% for InGaN at 1-240 suns, though both materials systems require significant development before these results could be achieved experimentally. For an experimental demonstration, CdSSe was selected due to its availability. Proof-of-concept CdSSe nanowire ensemble solar cells with two subcells were fabricated simultaneously on one substrate. I-V characterization under 1 sun AM1.5G conditions yielded open-circuit voltages (Voc) up to 307 and 173 mV and short-circuit current densities (Jsc) up to 0.091 and 0.974 mA/cm2 for the CdS- and CdSe-rich cells, respectively. Similar thin film cells were also fabricated for comparison. The nanowire cells showed substantially higher Voc than the film cells, which was attributed to higher material quality in the CdSSe absorber. I-V measurements were also conducted with optical filters to simulate a simple form of spectrum-splitting. The CdS-rich cells showed uniformly higher Voc and fill factor (FF) than the CdSe-rich cells, as expected due to their larger band gaps. This suggested higher power density was produced by the CdS-rich cells on the single-nanowire level, which is the principal benefit of spectrum-splitting. These results constitute a proof-of-concept experimental demonstration of the MILAMB approach to fabricating multiple cells for spectrum-splitting photovoltaics. Future systems based on this approach could help to reduce the cost and complexity of manufacturing spectrum-splitting photovoltaic systems and offer a low cost alternative to multi-junction tandems for achieving high efficiencies.
Preliminary design and simulation studies based on Anderson's model band line-ups were undertaken for CdPbS and InGaN alloys. Systems of six subcells obtained efficiencies in the 32-38% range for CdPbS and 34-40% for InGaN at 1-240 suns, though both materials systems require significant development before these results could be achieved experimentally. For an experimental demonstration, CdSSe was selected due to its availability. Proof-of-concept CdSSe nanowire ensemble solar cells with two subcells were fabricated simultaneously on one substrate. I-V characterization under 1 sun AM1.5G conditions yielded open-circuit voltages (Voc) up to 307 and 173 mV and short-circuit current densities (Jsc) up to 0.091 and 0.974 mA/cm2 for the CdS- and CdSe-rich cells, respectively. Similar thin film cells were also fabricated for comparison. The nanowire cells showed substantially higher Voc than the film cells, which was attributed to higher material quality in the CdSSe absorber. I-V measurements were also conducted with optical filters to simulate a simple form of spectrum-splitting. The CdS-rich cells showed uniformly higher Voc and fill factor (FF) than the CdSe-rich cells, as expected due to their larger band gaps. This suggested higher power density was produced by the CdS-rich cells on the single-nanowire level, which is the principal benefit of spectrum-splitting. These results constitute a proof-of-concept experimental demonstration of the MILAMB approach to fabricating multiple cells for spectrum-splitting photovoltaics. Future systems based on this approach could help to reduce the cost and complexity of manufacturing spectrum-splitting photovoltaic systems and offer a low cost alternative to multi-junction tandems for achieving high efficiencies.
ContributorsCaselli, Derek (Author) / Ning, Cun-Zheng (Thesis advisor) / Tao, Meng (Committee member) / Yu, Hongbin (Committee member) / Vasileska, Dragica (Committee member) / Arizona State University (Publisher)
Created2014
Description
Scientists around the world have been striving to develop artificial light-harvesting antenna model systems for energy and other light-driven biochemical applications. Among the various approaches to achieve this goal, one of the most promising is the assembly of structurally well-defined artificial light-harvesting antennas based on the principles of structural DNA nanotechnology. DNA has recently emerged as an extremely efficient material to organize molecules such as fluorophores and proteins on the nanoscale. It is desirable to develop a hybrid smart material by combining artificial antenna systems based on DNA with natural reaction center components, so that the material can be engineered to convert light energy to chemical energy via formation of a charge-separated state.
Presented here are a series of studies toward this goal. First, self-assembled seven-helix DNA bundles (7HB) with cyclic arrays of three distinct chromophores were developed. The spectral properties and energy transfer mechanisms in the artificial light-harvesting antenna were studied extensively using steady-state and time-resolved methods. Next, engineered cysteine residues in the reaction center of the purple photosynthetic bacterium Rhodobacter sphaeroides were each covalently conjugated to fluorophores in order to explore the spectral requirements for energy transfer between an artificial light harvesting system and the reaction center. Finally, a structurally well-defined and spectrally tunable artificial light-harvesting system was constructed, where multiple organic dyes were conjugated to 3-arm DNA nanostructure. A reaction center protein isolated from the purple photosynthetic bacterium Rhodobacter sphaeroides was linked to one end of the 3-arm junction to serve as the final acceptor, which converts the photonic energy absorbed by the chromophores into chemical energy by charge separation. This type of model system is required to understand how parameters such as geometry, spectral characteristics of the dyes, and conformational flexibility affect energy transfer, and can be used to inform the development of more complex model light-harvesting systems.
Presented here are a series of studies toward this goal. First, self-assembled seven-helix DNA bundles (7HB) with cyclic arrays of three distinct chromophores were developed. The spectral properties and energy transfer mechanisms in the artificial light-harvesting antenna were studied extensively using steady-state and time-resolved methods. Next, engineered cysteine residues in the reaction center of the purple photosynthetic bacterium Rhodobacter sphaeroides were each covalently conjugated to fluorophores in order to explore the spectral requirements for energy transfer between an artificial light harvesting system and the reaction center. Finally, a structurally well-defined and spectrally tunable artificial light-harvesting system was constructed, where multiple organic dyes were conjugated to 3-arm DNA nanostructure. A reaction center protein isolated from the purple photosynthetic bacterium Rhodobacter sphaeroides was linked to one end of the 3-arm junction to serve as the final acceptor, which converts the photonic energy absorbed by the chromophores into chemical energy by charge separation. This type of model system is required to understand how parameters such as geometry, spectral characteristics of the dyes, and conformational flexibility affect energy transfer, and can be used to inform the development of more complex model light-harvesting systems.
ContributorsDutta, Palash Kanti (Author) / Liu, Yan (Thesis advisor) / Yan, Hao (Thesis advisor) / Chen, Julian (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Deoxyribonucleic acid (DNA) has emerged as an excellent molecular building block for nanoconstruction in addition to its biological role of preserving genetic information. Its unique features such as predictable conformation and programmable intra- and inter-molecular Watson-Crick base pairing interactions make it a remarkable engineering material. A variety of convenient design rules and reliable assembly methods have been developed to engineer DNA nanostructures. The ability to create designer DNA architectures with accurate spatial control has allowed researchers to explore novel applications in directed material assembly, structural biology, biocatalysis, DNA
computing, nano-robotics, disease diagnosis, and drug delivery.
This dissertation focuses on developing the structural design rules for "static" DNA nano-architectures with increasing complexity. By using a modular self-assembly method, Archimedean tilings were achieved by association of different DNA motifs with designed arm lengths and inter-tile sticky end interactions. By employing DNA origami method, a new set of design rules was created to allow the scaffolds to travel in arbitrary directions in a designed geometry without local symmetry restrictions. Sophisticated wireframe structures of higher-order complexity were designed and constructed successfully. This dissertation also presents the use of "dynamic" DNA nanotechnology to construct DNA origami nanostructures with programmed reconfigurations.
computing, nano-robotics, disease diagnosis, and drug delivery.
This dissertation focuses on developing the structural design rules for "static" DNA nano-architectures with increasing complexity. By using a modular self-assembly method, Archimedean tilings were achieved by association of different DNA motifs with designed arm lengths and inter-tile sticky end interactions. By employing DNA origami method, a new set of design rules was created to allow the scaffolds to travel in arbitrary directions in a designed geometry without local symmetry restrictions. Sophisticated wireframe structures of higher-order complexity were designed and constructed successfully. This dissertation also presents the use of "dynamic" DNA nanotechnology to construct DNA origami nanostructures with programmed reconfigurations.
ContributorsZhang, Fei (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Gould, Ian (Committee member) / Zhang, Peiming (Committee member) / Arizona State University (Publisher)
Created2015