Matching Items (18)
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- All Subjects: nanotechnology
- Creators: Gould, Ian
- Creators: Tongay, Sefaattin
- Resource Type: Text
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
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
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
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
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 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
Description
Carbon nanomaterials have caught tremendous attention in the last few decades due to their unique physical and chemical properties. Tremendous effort has been made to develop new synthesis techniques for carbon nanomaterials and investigate their properties for different applications. In this work, carbon nanospheres (CNSs), carbon foams (CF), and single-walled carbon nanotubes (SWNTs) were studied for various applications, including water treatment, energy storage, actuators, and sensors.
A facile spray pyrolysis synthesis technique was developed to synthesize individual CNSs with specific surface area (SSA) up to 1106 m2/g. The hollow CNSs showed adsorption of up to 300 mg rhodamine B dye per gram carbon, which is more than 15 times higher than that observed for conventional carbon black. They were also evaluated as adsorbents for removal of arsenate and selenate from water and displayed good binding to both species, outperforming commercial activated carbons for arsenate removal in pH > 8. When evaluated as supercapacitor electrode materials, specific capacitances of up to 112 F/g at a current density of 0.1 A/g were observed. When used as Li-ion battery anode materials, the CNSs achieved a discharge capacity of 270 mAh/g at a current density of 372 mA/g (1C), which is 4-fold higher than that of commercial graphite anode.
Carbon foams were synthesized using direct pyrolysis and had SSA up to 2340 m2/g. When used as supercapacitor electrode materials, a specific capacitance up to 280 F/g was achieved at current density of 0.1 A/g and remained as high as 207 F/g, even at a high current density of 10 A/g.
A printed walking robot was made from common plastic films and coatings of SWNTs. The solid-state thermal bimorph actuators were multifunctional energy transducers powered by heat, light, or electricity. The actuators were also investigated for photo/thermal detection. Electrochemical actuators based on MnO2 were also studied for potential underwater applications.
SWNTs were also used to fabricate printable electrodes for trace Cr(VI) detection, which displayed sensitivity up to 500 nA/ppb for Cr(VI). The limit of detection was shown to be as low as 5 ppb. A flow detection system based on CNT/printed electrodes was also demonstrated.
A facile spray pyrolysis synthesis technique was developed to synthesize individual CNSs with specific surface area (SSA) up to 1106 m2/g. The hollow CNSs showed adsorption of up to 300 mg rhodamine B dye per gram carbon, which is more than 15 times higher than that observed for conventional carbon black. They were also evaluated as adsorbents for removal of arsenate and selenate from water and displayed good binding to both species, outperforming commercial activated carbons for arsenate removal in pH > 8. When evaluated as supercapacitor electrode materials, specific capacitances of up to 112 F/g at a current density of 0.1 A/g were observed. When used as Li-ion battery anode materials, the CNSs achieved a discharge capacity of 270 mAh/g at a current density of 372 mA/g (1C), which is 4-fold higher than that of commercial graphite anode.
Carbon foams were synthesized using direct pyrolysis and had SSA up to 2340 m2/g. When used as supercapacitor electrode materials, a specific capacitance up to 280 F/g was achieved at current density of 0.1 A/g and remained as high as 207 F/g, even at a high current density of 10 A/g.
A printed walking robot was made from common plastic films and coatings of SWNTs. The solid-state thermal bimorph actuators were multifunctional energy transducers powered by heat, light, or electricity. The actuators were also investigated for photo/thermal detection. Electrochemical actuators based on MnO2 were also studied for potential underwater applications.
SWNTs were also used to fabricate printable electrodes for trace Cr(VI) detection, which displayed sensitivity up to 500 nA/ppb for Cr(VI). The limit of detection was shown to be as low as 5 ppb. A flow detection system based on CNT/printed electrodes was also demonstrated.
ContributorsWang, Chengwei, Ph.D (Author) / Chan, Candace K. (Thesis advisor) / Tongay, Sefaattin (Committee member) / Wang, Qing Hua (Committee member) / Seo, Dong (Committee member) / Arizona State University (Publisher)
Created2015
Description
Graphene is a very strong two-dimensional material with a lot of potential applications in microelectromechanical systems (MEMS). In this research, graphene is being optimized for use in a 5 m x 5 m graphene resonator. To work properly, this graphene resonator must have a uniform strain across all manufactured devices. To reduce strain induced in graphene sheets grown for use in these resonators, evaporated platinum has been used in this investigation due to its relatively lower surface roughness compared to copper films. The final goal is to have the layer of ultrathin platinum (<=200 nm) deposited on the MEMS graphene resonator and used to grow graphene directly onto the devices to remove the manual transfer step due to its inscalability. After growth, graphene is coated with polymer and the platinum is then etched. This investigation concentrated on the transfer process of graphene onto Si/SiO2 substrate from the platinum films. It was determined that the ideal platinum etchant was aqua regia at a volumetric ratio of 6:3:1 (H2O:HCl:HNO3). This concentration was dilute enough to preserve the polymer and graphene layer, but strong enough to etch within a day. Type and thickness of polymer support layers were also investigated. PMMA at a thickness of 200 nm was ideal because it was easy to remove with acetone and strong enough to support the graphene during the etch process. A reference growth recipe was used in this investigation, but now that the transfer has been demonstrated, growth can be optimized for even thinner films.
ContributorsCayll, David Richard (Author) / Tongay, Sefaattin (Thesis director) / Lee, Hyunglae (Committee member) / Mechanical and Aerospace Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
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 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.
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