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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

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
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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

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
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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

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
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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

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
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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

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.
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
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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

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.
ContributorsZhang, Fei (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Gould, Ian (Committee member) / Zhang, Peiming (Committee member) / Arizona State University (Publisher)
Created2015
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Description
This thesis summarizes the research work carried out on design, modeling and simulation of semiconductor nanophotonic devices. The research includes design of nanowire (NW) lasers, modeling of active plasmonic waveguides, design of plasmonic nano-lasers, and design of all-semiconductor plasmonic systems. For the NW part, a comparative study of electrical injection

This thesis summarizes the research work carried out on design, modeling and simulation of semiconductor nanophotonic devices. The research includes design of nanowire (NW) lasers, modeling of active plasmonic waveguides, design of plasmonic nano-lasers, and design of all-semiconductor plasmonic systems. For the NW part, a comparative study of electrical injection in the longitudinal p-i-n and coaxial p-n core-shell NWs was performed. It is found that high density carriers can be efficiently injected into and confined in the core-shell structure. The required bias voltage and doping concentrations in the core-shell structure are smaller than those in the longitudinal p-i-n structure. A new device structure with core-shell configuration at the p and n contact regions for electrically driven single NW laser was proposed. Through a comprehensive design trade-off between threshold gain and threshold voltage, room temperature lasing has been proved in the laser with low threshold current and large output efficiency. For the plasmonic part, the propagation of surface plasmon polariton (SPP) in a metal-semiconductor-metal structure where semiconductor is highly excited to have an optical gain was investigated. It is shown that near the resonance the SPP mode experiences an unexpected giant modal gain that is 1000 times of the material gain in the semiconductor and the corresponding confinement factor is as high as 105. The physical origin of the giant modal gain is the slowing down of the average energy propagation in the structure. Secondly, SPP modes lasing in a metal-insulator-semiconductor multi-layer structure was investigated. It is shown that the lasing threshold can be reduced by structural optimization. A specific design example was optimized using AlGaAs/GaAs/AlGaAs single quantum well sandwiched between silver layers. This cavity has a physical volume of 1.5×10-4 λ03 which is the smallest nanolaser reported so far. Finally, the all-semiconductor based plasmonics was studied. It is found that InAs is superior to other common semiconductors for plasmonic application in mid-infrared range. A plasmonic system made of InAs, GaSb and AlSb layers, consisting of a plasmonic source, waveguide and detector was proposed. This on-chip integrated system is realizable in a single epitaxial growth process.
ContributorsLi, Debin (Author) / Ning, Cun-Zheng (Thesis advisor) / Zhang, Yong-Hang (Committee member) / Balanis, Constantine A (Committee member) / Yu, Hongbin (Committee member) / Arizona State University (Publisher)
Created2012
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Description
To detect and resolve sub-wavelength features at optical frequencies, beyond the diffraction limit, requires sensors that interact with the electromagnetic near-field of those features. Most instruments operating in this modality scan a single detector element across the surface under inspection because the scattered signals from a multiplicity of such elements

To detect and resolve sub-wavelength features at optical frequencies, beyond the diffraction limit, requires sensors that interact with the electromagnetic near-field of those features. Most instruments operating in this modality scan a single detector element across the surface under inspection because the scattered signals from a multiplicity of such elements would end up interfering with each other. However, an alternative massively parallelized configuration, consisting of a remotely interrogating array of dipoles, capable of interrogating multiple adjacent areas of the surface at the same time, was proposed in 2002.

In the present work a remotely interrogating slot antenna inside a 60nm silver slab is designed which increases the signal to noise ratio of the original system. The antenna is tuned to resonance at 600nm range by taking advantage of the plasmon resonance properties of the metal’s negative permittivity and judicious shaping of the slot element. Full-physics simulations show the capability of detecting an 8nm particle using red light illumination. The sensitivity to the λ/78 particle is attained by detecting the change induced on the antenna’s far field signature by the proximate particle, a change that is 15dB greater than the scattering signature of the particle by itself.

To verify the capabilities of this technology in a readily accessible experimental environment, a radiofrequency scale model is designed using a meta-material to mimic the optical properties of silver in the 2GHz to 5GHz range. Various approaches to the replication of the metal’s behavior are explored in a trade-off between fidelity to the metal’s natural plasmon response, desired bandwidth of the demonstration, and

ii

manufacturability of the meta-material. The simulation and experimental results successfully verify the capability of the proposed near-field sensor in sub-wavelength detection and imaging not only as a proof of concept for optical frequencies but also as a potential imaging device for radio frequencies.
ContributorsMostafavi, Mahkamehossadat (Author) / Diaz, Rodolfo E (Thesis advisor) / Pan, George W (Committee member) / Aberle, James T (Committee member) / Ning, Cun-Zheng (Committee member) / Arizona State University (Publisher)
Created2016
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Description
Semiconductor nanolasers, as a frontier subject has drawn a great deal of attention over the past decade. Semiconductor nanolasers are compatible with on-chip integrations towards the ultimate realization of photonic integrated circuits. However, innovative approaches are strongly required to overcome the limitation of lattice-mismatch issues. In this dissertation, two alternative

Semiconductor nanolasers, as a frontier subject has drawn a great deal of attention over the past decade. Semiconductor nanolasers are compatible with on-chip integrations towards the ultimate realization of photonic integrated circuits. However, innovative approaches are strongly required to overcome the limitation of lattice-mismatch issues. In this dissertation, two alternative approaches are employed to overcome the lattice-mismatch issues. i) By taking advantage of nanowires or nanobelts techniques, flexibility in bandgap engineering has been greatly expanded, resulting in the nanolasers with wide wavelength coverage and tunability. Simultaneous two-color lasing in green and red is firstly achieved from monolithic cadmium sulfide selenide nanosheets. The wavelength separation is up to 97 nm at room temperature, larger than the gain bandwidth of a single semiconductor material in the visible wavelength range. The strategies adopted for two-color lasers eventually leads to the realization of simultaneous red, green and blue lasing and white lasing from a single zinc cadmium sulfide selenide nanosheet with color tunability in the full visible range, making a major milestone in the ultimate solution of laser illumination and laser display. In addition, with the help of nanowire techniques, material emission has been extended to mid-infrared range, enabling lasing at ~3µm from single lead sulfide subwavelength wires at 180 K. The cavity volume of the subwavelength laser is down to 0.44 λ3 and the wavelength tuning range is over 270 nm through the thermo-optic mechanism, exhibiting considerable potentials for on-chip applications in mid-infrared wavelength ranges. ii) By taking advantage of membrane transfer techniques, heterogeneous integration of compound semiconductor and waveguide material becomes possible, enabling the successful fabrication of membrane based nano-ring lasers on a dielectric substrate. Thin membranes with total thickness of ~200nm are first released from the original growth substrate and then transferred onto a receiving substrate through a generally applicable membrane transfer method. Nano-ring arrays are then defined by photolithography with an individual radius of 750 nm and a radial thickness of 400-500 nm. As a result, single mode lasing is achieved on individual nano-ring lasers at ~980 nm with cavity volumes down to 0.24 λ3, providing a general avenue for future heterogeneous integration of nanolasers on silicon substrates.
ContributorsFan, Fan (Author) / Ning, Cun-Zheng (Thesis advisor) / Balanis, Constantine A (Committee member) / Palais, Joseph C. (Committee member) / Yu, Hongbin (Committee member) / Arizona State University (Publisher)
Created2016
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Description
The energy band gap of a semiconductor material critically influences the operating wavelength of an optoelectronic device. Realization of any desired band gap, or even spatially graded band gaps, is important for applications such as lasers, light-emitting diodes (LEDs), solar cells, and detectors. Compared to thin films, nanowires offer greater

The energy band gap of a semiconductor material critically influences the operating wavelength of an optoelectronic device. Realization of any desired band gap, or even spatially graded band gaps, is important for applications such as lasers, light-emitting diodes (LEDs), solar cells, and detectors. Compared to thin films, nanowires offer greater flexibility for achieving a variety of alloy compositions. Furthermore, the nanowire geometry permits simultaneous incorporation of a wide range of compositions on a single substrate. Such controllable alloy composition variation can be realized either within an individual nanowire or between distinct nanowires across a substrate. This dissertation explores the control of spatial composition variation in ternary alloy nanowires. Nanowires were grown by the vapor-liquid-solid (VLS) mechanism using chemical vapor deposition (CVD). The gas-phase supersaturation was considered in order to optimize the deposition morphology. Composition and structure were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive x-ray spectroscopy (EDS), and x-ray diffraction (XRD). Optical properties were investigated through photoluminescence (PL) measurements. The chalcogenides selected as alloy endpoints were lead sulfide (PbS), cadmium sulfide (CdS), and cadmium selenide (CdSe). Three growth modes of PbS were identified, which included contributions from spontaneously generated catalyst. The resulting wires were found capable of lasing with wavelengths over 4000 nm, representing the longest known wavelength from a sub-wavelength wire. For CdxPb1-xS nanowires, it was established that the cooling process significantly affects the alloy composition and structure. Quenching was critical to retain metastable alloys with x up to 0.14, representing a new composition in nanowire form. Alternatively, gradual cooling caused phase segregation, which created heterostructures with light emission in both the visible and mid-infrared regimes. The CdSSe alloy system was fully explored for spatial composition variation. CdSxSe1-x nanowires were grown with composition variation across the substrate. Subsequent contact printing preserved the designed composition gradient and led to the demonstration of a variable wavelength photodetector device. CdSSe axial heterostructure nanowires were also achieved. The growth process involved many variables, including a deliberate and controllable change in substrate temperature. As a result, both red and green light emission was detected from single nanowires.
ContributorsNichols, Patricia (Author) / Ning, Cun-Zheng (Thesis advisor) / Carpenter, Ray (Committee member) / Bennett, Peter (Committee member) / Smith, David (Committee member) / Arizona State University (Publisher)
Created2012