Matching Items (8)
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- All Subjects: nanotechnology
- Creators: Chen, Julian
Description
DNA has recently emerged as an extremely promising material to organize molecules on nanoscale. The reliability of base recognition, self-assembling behavior, and attractive structural properties of DNA are of unparalleled value in systems of this size. DNA scaffolds have already been used to organize a variety of molecules including nanoparticles and proteins. New protein-DNA bio-conjugation chemistries make it possible to precisely position proteins and other biomolecules on underlying DNA scaffolds, generating multi-biomolecule pathways with the ability to modulate inter-molecular interactions and the local environment. This dissertation focuses on studying the application of using DNA nanostructure to direct the self-assembly of other biomolecular networks to translate biochemical pathways to non-cellular environments. Presented here are a series of studies toward this application. First, a novel strategy utilized DNA origami as a scaffold to arrange spherical virus capsids into one-dimensional arrays with precise nanoscale positioning. This hierarchical self-assembly allows us to position the virus particles with unprecedented control and allows the future construction of integrated multi-component systems from biological scaffolds using the power of rationally engineered DNA nanostructures. Next, discrete glucose oxidase (GOx)/ horseradish peroxidase (HRP) enzyme pairs were organized on DNA origami tiles with controlled interenzyme spacing and position. This study revealed two different distance-dependent kinetic processes associated with the assembled enzyme pairs. Finally, a tweezer-like DNA nanodevice was designed and constructed to actuate the activity of an enzyme/cofactor pair. Using this approach, several cycles of externally controlled enzyme inhibition and activation were successfully demonstrated. This principle of responsive enzyme nanodevices may be used to regulate other types of enzymes and to introduce feedback or feed-forward control loops.
ContributorsLiu, Minghui (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Zhang, Peiming (Committee member) / Arizona State University (Publisher)
Created2013
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
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
Programmable Metallization Cell (PMC) is a technology platform which utilizes mass transport in solid or liquid electrolyte coupled with electrochemical (redox) reactions to form or remove nanoscale metallic electrodeposits on or in the electrolyte. The ability to redistribute metal mass and form metallic nanostructure in or on a structure in situ, via the application of a bias on laterally placed electrodes, creates a large number of promising applications. A novel PMC-based lateral microwave switch was fabricated and characterized for use in microwave systems. It has demonstrated low insertion loss, high isolation, low voltage operation, low power and low energy consumption, and excellent linearity. Due to its non-volatile nature the switch operates with fewer biases and its simple planar geometry makes possible innovative device structures which can be potentially integrated into microwave power distribution circuits. PMC technology is also used to develop lateral dendritic metal electrodes. A lateral metallic dendritic network can be grown in a solid electrolyte (GeSe) or electrodeposited on SiO2 or Si using a water-mediated method. These dendritic electrodes grown in a solid electrolyte (GeSe) can be used to lower resistances for applications like self-healing interconnects despite its relatively low light transparency; while the dendritic electrodes grown using water-mediated method can be potentially integrated into solar cell applications, like replacing conventional Ag screen-printed top electrodes as they not only reduce resistances but also are highly transparent. This research effort also laid a solid foundation for developing dendritic plasmonic structures. A PMC-based lateral dendritic plasmonic structure is a device that has metallic dendritic networks grown electrochemically on SiO2 with a thin layer of surface metal nanoparticles in liquid electrolyte. These structures increase the distribution of particle sizes by connecting pre-deposited Ag nanoparticles into fractal structures and result in three significant effects, resonance red-shift, resonance broadening and resonance enhancement, on surface plasmon resonance for light trapping simultaneously, which can potentially enhance thin film solar cells' performance at longer wavelengths.
ContributorsRen, Minghan (Author) / Kozicki, Michael (Thesis advisor) / Schroder, Dieter (Committee member) / Roedel, Ronald (Committee member) / Barnaby, Hugh (Committee member) / Arizona State University (Publisher)
Created2011
Description
This dissertation addresses challenges pertaining to multi-junction (MJ) solar cells from material development to device design and characterization. Firstly, among the various methods to improve the energy conversion efficiency of MJ solar cells using, a novel approach proposed recently is to use II-VI (MgZnCd)(SeTe) and III-V (AlGaIn)(AsSb) semiconductors lattice-matched on GaSb or InAs substrates for current-matched subcells with minimal defect densities. CdSe/CdTe superlattices are proposed as a potential candidate for a subcell in the MJ solar cell designs using this material system, and therefore the material properties of the superlattices are studied. The high structural qualities of the superlattices are obtained from high resolution X-ray diffraction measurements and cross-sectional transmission electron microscopy images. The effective bandgap energies of the superlattices obtained from the photoluminescence (PL) measurements vary with the layer thicknesses, and are smaller than the bandgap energies of either the constituent material. Furthermore, The PL peak position measured at the steady state exhibits a blue shift that increases with the excess carrier concentration. These results confirm a strong type-II band edge alignment between CdSe and CdTe. The valence band offset between unstrained CdSe and CdTe is determined as 0.63 eV±0.06 eV by fitting the measured PL peak positions using the Kronig-Penney model. The blue shift in PL peak position is found to be primarily caused by the band bending effect based on self-consistent solutions of the Schrödinger and Poisson equations. Secondly, the design of the contact grid layout is studied to maximize the power output and energy conversion efficiency for concentrator solar cells. Because the conventional minimum power loss method used for the contact design is not accurate in determining the series resistance loss, a method of using a distributed series resistance model to maximize the power output is proposed for the contact design. It is found that the junction recombination loss in addition to the series resistance loss and shadowing loss can significantly affect the contact layout. The optimal finger spacing and maximum efficiency calculated by the two methods are close, and the differences are dependent on the series resistance and saturation currents of solar cells. Lastly, the accurate measurements of external quantum efficiency (EQE) are important for the design and development of MJ solar cells. However, the electrical and optical couplings between the subcells have caused EQE measurement artifacts. In order to interpret the measurement artifacts, DC and small signal models are built for the bias condition and the scan of chopped monochromatic light in the EQE measurements. Characterization methods are developed for the device parameters used in the models. The EQE measurement artifacts are found to be caused by the shunt and luminescence coupling effects, and can be minimized using proper voltage and light biases. Novel measurement methods using a pulse voltage bias or a pulse light bias are invented to eliminate the EQE measurement artifacts. These measurement methods are nondestructive and easy to implement. The pulse voltage bias or pulse light bias is superimposed on the conventional DC voltage and light biases, in order to control the operating points of the subcells and counterbalance the effects of shunt and luminescence coupling. The methods are demonstrated for the first time to effectively eliminate the measurement artifacts.
ContributorsLi, Jingjing (Author) / Zhang, Yong-Hang (Thesis advisor) / Tao, Meng (Committee member) / Schroder, Dieter (Committee member) / Vasileska, Dragica (Committee member) / Arizona State University (Publisher)
Created2012
Description
To extend the lifetime of complementary metal-oxide-semiconductors (CMOS), emerging process techniques are being proposed to conquer the manufacturing difficulties. New structures and materials are proposed with superior electrical properties to traditional CMOS, such as strain technology and feedback field-effect transistor (FB-FET). To continue the design success and make an impact on leading products, advanced circuit design exploration must begin concurrently with early silicon development. Therefore, an accurate and scalable model is desired to correctly capture those effects and flexible to extend to alternative process choices. For example, strain technology has been successfully integrated into CMOS fabrication to improve transistor performance but the stress is non-uniformly distributed in the channel, leading to systematic performance variations. In this dissertation, a new layout-dependent stress model is proposed as a function of layout, temperature, and other device parameters. Furthermore, a method of layout decomposition is developed to partition the layout into a set of simple patterns for model extraction. These solutions significantly reduce the complexity in stress modeling and simulation. On the other hand, semiconductor devices with self-feedback mechanisms are emerging as promising alternatives to CMOS. Fe-FET was proposed to improve the switching by integrating a ferroelectric material as gate insulator in a MOSFET structure. Under particular circumstances, ferroelectric capacitance is effectively negative, due to the negative slope of its polarization-electrical field curve. This property makes the ferroelectric layer a voltage amplifier to boost surface potential, achieving fast transition. A new threshold voltage model for Fe-FET is developed, and is further revealed that the impact of random dopant fluctuation (RDF) can be suppressed. Furthermore, through silicon via (TSV), a key technology that enables the 3D integration of chips, is studied. TSV structure is usually a cylindrical metal-oxide-semiconductors (MOS) capacitor. A piecewise capacitance model is proposed for 3D interconnect simulation. Due to the mismatch in coefficients of thermal expansion (CTE) among materials, thermal stress is observed in TSV process and impacts neighboring devices. The stress impact is investigated to support the interaction between silicon process and IC design at the early stage.
ContributorsWang, Chi-Chao (Author) / Cao, Yu (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Clark, Lawrence (Committee member) / Schroder, Dieter (Committee member) / Arizona State University (Publisher)
Created2011
Description
The discovery of DNA helical structure opened the door of modern molecular biology. Ned Seeman utilized DNA as building block to construct different nanoscale materials, and introduced a new field, know as DNA nanotechnology. After several decades of development, different DNA structures had been created, with different dimension, different morphology and even with complex curvatures. In addition, after construction of enough amounts DNA structure candidates, DNA structure template, with excellent spatial addressability, had been used to direct the assembly of different nanomaterials, including nanoparticles and proteins, to produce different functional nanomaterials. However there are still many challenges to fabricate functional DNA nanostructures. The first difficulty is that the present finite sized template dimension is still very small, usually smaller than 100nm, which will limit the application for large amount of nanomaterials assembly or large sized nanomaterials assembly. Here we tried to solve this problem through developing a new method, superorigami, to construct finite sized DNA structure with much larger dimension, which can be as large as 500nm. The second problem will be explored the ability of DNA structure to assemble inorganic nanomaterials for novel photonic or electronic properties. Here we tried to utilize DNA Origami method to assemble AuNPs with controlled 3D spacial position for possible chiral photonic complex. We also tried to assemble SWNT with discrete length for possible field effect transistor device. In addition, we tried to mimic in vivo compartment with DNA structure to study internalized enzyme behavior. From our results, constructed DNA cage origami can protect encapsulated enzyme from degradation, and internalized enzyme activity can be boosted for up to 10 folds. In summary, DNA structure can serve as an ideal template for construction of functional nanomaterials with lots of possibilities to be explored.
ContributorsZhao, Zhao (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Seo, Dong-Kyun (Committee member) / Arizona State University (Publisher)
Created2013