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- Genre: Academic theses
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Description
This thesis describes several approaches to next generation DNA sequencing via tunneling current method based on a Scanning Tunneling Microscope system. In chapters 5 and 6, preliminary results have shown that DNA bases could be identified by their characteristic tunneling signals. Measurements taken in aqueous buffered solution showed that single base resolution could be achieved with economic setups. In chapter 7, it is illustrated that some ongoing measurements are indicating the sequence readout by making linear scan on a piece of short DNA oligomer. However, to overcome the difficulties of controlling DNA especially ssDNA movement, it is much better to have the tunneling measurement incorporated onto a robust nanopore device to realize sequential reading of the DNA sequence while it is being translocated.
ContributorsHuang, Shuo (Author) / Lindsay, Stuart (Thesis advisor) / Sankey, Otto (Committee member) / Tao, Nongjian (Committee member) / Drucker, Jeff (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2011
Description
In this work, a new method, "Nanobonding" [1,2] is conceived and researched to bond Si-based surfaces, via nucleation and growth of a 2 D silicon oxide SiOxHx interphase connecting the surfaces at the nanoscale across macroscopic domains. Nanobonding cross-bridges two smooth surfaces put into mechanical contact in an O2/H2O mixed ambient below T <200 °C via arrays of SiOxHx molecules connecting into a continuous macroscopic bonding interphase. Nano-scale surface planarization via wet chemical processing and new spin technology are compared via Tapping Mode Atomic Force Microscopy (TMAFM) , before and after nano-bonding. Nanobonding uses precursor phases, 2D nano-films of beta-cristobalite (beta-c) SiO2, nucleated on Si(100) via the Herbots-Atluri (H-A) method [1]. beta-c SiO2 on Si(100) is ordered and flat with atomic terraces over 20 nm wide, well above 2 nm found in native oxides. When contacted with SiO2 this ultra-smooth nanophase can nucleate and grow domains with cross-bridging molecular strands of hydroxylated SiOx, instead of point contacts. The high density of molecular bonds across extended terraces forms a strong bond between Si-based substrates, nano- bonding [2] the Si and silica. A new model of beta-cristobalite SiO2 with its <110> axis aligned along Si[100] direction is simulated via ab-initio methods in a nano-bonded stack with beta-c SiO2 in contact with amorphous SiO2 (a-SiO2), modelling cross-bridging molecular bonds between beta-c SiO2 on Si(100) and a-SiO2 as during nanobonding. Computed total energies are compared with those found for Si(100) and a-SiO2 and show that the presence of two lattice cells of !-c SiO2 on Si(100) and a-SiO2 lowers energy when compared to Si(100)/ a-SiO2 Shadow cone calculations on three models of beta-c SiO2 on Si(100) are compared with Ion Beam Analysis of H-A processed Si(100). Total surface energy measurements via 3 liquid contact angle analysis of Si(100) after H-A method processing are also compared. By combining nanobonding experiments, TMAFM results, surface energy data, and ab-initio calculations, an atomistic model is derived and nanobonding is optimized. [1] US Patent 6,613,677 (9/2/03), 7,851,365 (12/14/10), [2] Patent Filed: 4/30/09, 10/1/2011
ContributorsWhaley, Shawn D (Author) / Culbertson, Robert J. (Thesis advisor) / Herbots, Nicole (Committee member) / Rez, Peter (Committee member) / Marzke, Robert F (Committee member) / Lindsay, Stuart (Committee member) / Chamberlin, Ralph V (Committee member) / Arizona State University (Publisher)
Created2011
Description
This thesis describes several experiments based on carbon nanotube nanofludic devices and field-effect transistors. The first experiment detected ion and molecule translocation through one single-walled carbon nanotube (SWCNT) that spans a barrier between two fluid reservoirs. The electrical ionic current is measured. Translocation of small single stranded DNA oligomers is marked by large transient increases in current through the tube and confirmed by a PCR (polymerase chain reaction) analysis. Carbon nanotubes simplify the construction of nanopores, permit new types of electrical measurement, and open new avenues for control of DNA translocation. The second experiment constructed devices in which the interior of a single-walled carbon nanotube field-effect transistor (CNT-FET) acts as a nanofluidic channel that connects two fluid reservoirs, permitting measurement of the electronic properties of the SWCNT as it is wetted by an analyte. Wetting of the inside of the SWCNT by water turns the transistor on, while wetting of the outside has little effect. This finding may provide a new method to investigate water behavior at nanoscale. This also opens a new avenue for building sensors in which the SWCNT functions as an electronic detector. This thesis also presents some experiments that related to nanofabrication, such as construction of FET with tin sulfide (SnS) quantum ribbon. This work demonstrates the application of solution processed IV-VI semiconductor nanostructures in nanoscale devices.
ContributorsCao, Zhai (Author) / Lindsay, Stuart (Thesis advisor) / Vaiana, Sara (Committee member) / Ros, Robert (Committee member) / Marzke, Robert (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
he accurate simulation of many-body quantum systems is a challenge for computational physics. Quantum Monte Carlo methods are a class of algorithms that can be used to solve the many-body problem. I study many-body quantum systems with Path Integral Monte Carlo techniques in three related areas of semiconductor physics: (1) the role of correlation in exchange coupling of spins in double quantum dots, (2) the degree of correlation and hyperpolarizability in Stark shifts in InGaAs/GaAs dots, and (3) van der Waals interactions between 1-D metallic quantum wires at finite temperature. The two-site model is one of the simplest quantum problems, yet the quantitative mapping from a three-dimensional model of a quantum double dot to an effective two-site model has many subtleties requiring careful treatment of exchange and correlation. I calculate exchange coupling of a pair of spins in a double dot from the permutations in a bosonic path integral, using Monte Carlo method. I also map this problem to a Hubbard model and find that exchange and correlation renormalizes the model parameters, dramatically decreasing the effective on-site repulsion at larger separations. Next, I investigated the energy, dipole moment, polarizability and hyperpolarizability of excitonic system in InGaAs/GaAs quantum dots of different shapes and successfully give the photoluminescence spectra for different dots with electric fields in both the growth and transverse direction. I also showed that my method can deal with the higher-order hyperpolarizability, which is most relevant for fields directed in the lateral direction of large dots. Finally, I show how van der Waals interactions between two metallic quantum wires change with respect to the distance between them. Comparing the results from quantum Monte Carlo and the random phase approximation, I find similar power law dependance. My results for the calculation in quasi-1D and exact 1D wires include the effect of temperature, which has not previously been studied.
ContributorsZhang, Lei (Author) / Shumway, John (Thesis advisor) / Schmidt, Kevin (Committee member) / Bennet, Peter (Committee member) / Menéndez, Jose (Committee member) / Drucker, Jeff (Committee member) / Arizona State University (Publisher)
Created2011
Description
Nucleosomes are the basic repetitive unit of eukaryotic chromatin and are responsible for packing DNA inside the nucleus of the cell. They consist of a complex of eight histone proteins (two copies of four proteins H2A, H2B, H3 and H4) around which 147 base pairs of DNA are wrapped in ~1.67 superhelical turns. Although the nucleosomes are stable protein-DNA complexes, they undergo spontaneous conformational changes that occur in an asynchronous fashion. This conformational dynamics, defined by the "site-exposure" model, involves the DNA unwrapping from the protein core and exposing itself transiently before wrapping back. Physiologically, this allows regulatory proteins to bind to their target DNA sites during cellular processes like replication, DNA repair and transcription. Traditional biochemical assays have stablished the equilibrium constants for the accessibility to various sites along the length of the nucleosomal DNA, from its end to the middle of the dyad axis. Using fluorescence correlation spectroscopy (FCS), we have established the position dependent rewrapping rates for nucleosomes. We have also used Monte Carlo simulation methods to analyze the applicability of FRET fluctuation spectroscopy towards conformational dynamics, specifically motivated by nucleosome dynamics. Another important conformational change that is involved in cellular processes is the disassembly of nucleosome into its constituent particles. The exact pathway adopted by nucleosomes is still not clear. We used dual color fluorescence correlation spectroscopy to study the intermediates during nucleosome disassembly induced by changing ionic strength. Studying the nature of nucleosome conformational change and the kinetics is very important in understanding gene expression. The results from this thesis give a quantitative description to the basic unit of the chromatin.
ContributorsGurunathan, Kaushik (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Woodbury, Neal (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2011
Description
Nanofluidic devices in which one single-walled carbon nanotube (SWCNT) spans a barrier between two fluid reservoirs were constructed, enabling direct electrical measurement of the transport of ions and molecules. Ion current through these devices is about 2 orders of magnitude larger than that predicted from the bulk resistivity of the electrolyte. Electroosmosis drives excess current, carried by cations, and is found to be the origin of giant ionic current through SWCNT as shown by building an ionic field-effect transistor with a gate electrode embedded in the fluid barrier. Wetting of inside of the semi-conducting SWCNT by water showed the change of its electronic property, turning the electronic SWCNT field-effect transistor to "on" state. These findings provide a new method to investigate and control the ion and molecule behavior at nanoscale.
ContributorsPang, Pei (Author) / Lindsay, Stuart (Thesis advisor) / Ros, Robert (Committee member) / Shumway, John (Committee member) / Tao, Nongjian (Committee member) / Menéndez, Jose (Committee member) / Arizona State University (Publisher)
Created2011
Description
ABSTRACT Group III-nitride semiconductor materials have been commercially used in fabrication of light-emitting diodes (LEDs) and laser diodes (LDs) covering the spectral range from UV to visible and infrared, and exhibit unique properties suitable for modern optoelectronic applications. Great advances have recently happened in the research and development in high-power and high-efficiency blue-green-white LEDs, blue LDs and other optoelectronic applications. However, there are still many unsolved challenges with these materials. In this dissertation, several issues concerning structural, electronic and optical properties of III-nitrides have been investigated using a combination of transmission electron microscopy (TEM), electron holography (EH) and cathodoluminescence (CL) techniques. First, a trend of indium chemical inhomogeneity has been found as the indium composition increases for the InGaN epitaxial layers grown by hydride vapor phase epitaxy. Second, different mechanisms contributing to the strain relaxation have been studied for non-polar InGaN epitaxial layers grown on zinc oxide (ZnO) substrate. Third, various structural morphologies of non-polar InGaN epitaxial layers grown on free-standing GaN substrate have been investigated. Fourth, the effect of the growth temperature on the performance of GaN lattice-matched InAlN electron blocking layers has been studied. Finally, the electronic and optical properties of GaN nanowires containing a AlN/GaN superlattice structure have been investigated showing relatively small internal electric field and superlattice- and defect-related emissions along the nanowires.
ContributorsSun, Kewei (Author) / Ponce, Fernando (Thesis advisor) / Smith, David (Committee member) / Treacy, Michael (Committee member) / Drucker, Jeffery (Committee member) / Schmidt, Kevin (Committee member) / Arizona State University (Publisher)
Created2011
Description
One of the most important issues in femtosecond free electron laser X-ray diraction is to reconstruct the 3D charge density of molecule from a mass of diraction snapshots. In order to determine the orientation of single molecule from diraction patterns, we rst determine the moments and products of inertia of this from 2D experiment data (diraction patterns or EM images to obtain the elements of the inertia tensor. If diraction patterns from uniformly random orientations or some preferred orientations are collected, the principal axes of the molecule can be extracted, together with the Euler angles which relate the principal axes of the molecule to the laboratory frame axes. This is achieved by nding the maximum and minimum values for the measured moments from many single-molecule patterns. Simulations for GroEL protein indicates that the calculation of the autocorrelation help eliminate the Poisson noise in Cryo- EM images and can make correct orientation determination. The eect of water jacket surrounding the protein molecule is studied based on molecular dynamics simulation result. The intensities from water and interference is found to suppress those from protein itself. A method is proposed and applied to the simulation data to show the possibility for it to overcome the water background problem. The scattering between Bragg re ections from nanocrystals is used to aid solution of the phase problem. We describe a method for reconstructing the charge density of a typical molecule within a single unit cell, if suciently nely-sampled diraction data are available from many nanocrystals of dierent sizes lying in the same orientations without knowledge of the distribution of particle size or requiring atomic-resolution data. Triple correlation of the diraction patterns are made use of to reconiii
ContributorsWang, Xiaoyu (Author) / Spence, John C.H. (Thesis advisor) / Schmidt, Kevin (Committee member) / Doak, R. Bruce (Committee member) / Weierstall, Uwe (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2011
Description
This dissertation describes the work on two projects which involves measuring molecular conductance and studying their properties on the nanoscale using various Scanning Tunneling Microscopy (STM) techniques. The first molecule studied was a porphyrin-fullerene moiety known as a molecular Dyad for photovoltaic applications. This project is further divided into two section, the first one involving the characterization of the Dyad monolayers and conductance measurement in the dark. The Dyads are designed to form charge separated states on illumination. The lifetime of the charged states have been measured efficiently but the single-molecule conductance through the molecules have yet to be characterized. The second part of the project describes the set-up of a novel sample stage which enables the study of molecular conductance under illumination. This part also describes the subsequent study of the molecule under illumination and the observation of a unique charge-separated state. It also contains the verification of the presence of this charge-separated using other characterization techniques like transient absorption spectroscopy. The second project described in the dissertation was studying and comparing the predicted rectifying nature of two molecules, identical in every way except for one stereocenter. This project describes the formation of monolayers of the molecule on gold and then studying and analyzing the current-voltage characteristics of the molecules and looking for rectification. Both the molecules proved to be rectifying, one more than the other as predicted by theoretical calculations.
ContributorsBhattacharyya, Shreya (Author) / Lindsay, Stuart (Thesis advisor) / Moore, Ana (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2011
Description
Solution conformations and dynamics of proteins and protein-DNA complexes are often difficult to predict from their crystal structures. The crystal structure only shows a snapshot of the different conformations these biological molecules can have in solution. Multiple different conformations can exist in solution and potentially have more importance in the biological activity. DNA sliding clamps are a family of proteins with known crystal structures. These clamps encircle the DNA and enable other proteins to interact more efficiently with the DNA. Eukaryotic PCNA and prokaryotic β clamp are two of these clamps, some of the most stable homo-oligomers known. However, their solution stability and conformational equilibrium have not been investigated in depth before. Presented here are the studies involving two sliding clamps: yeast PCNA and bacterial β clamp. These studies show that the β clamp has a very different solution stability than PCNA. These conclusions were reached through various different fluorescence-based experiments, including fluorescence correlation spectroscopy (FCS), Förster resonance energy transfer (FRET), single molecule fluorescence, and various time resolved fluorescence techniques. Interpretations of these, and all other, fluorescence-based experiments are often affected by the properties of the fluorophores employed. Often the fluorescence properties of these fluorophores are influenced by their microenvironments. Fluorophores are known to sometimes interact with biological molecules, and this can have pronounced effects on the rotational mobility and photophysical properties of the dye. Misunderstanding the effect of these photophysical and rotational properties can lead to a misinterpretation of the obtained data. In this thesis, photophysical behaviors of various organic dyes were studied in the presence of deoxymononucleotides to examine more closely how interactions between fluorophores and DNA bases can affect fluorescent properties. Furthermore, the properties of cyanine dyes when bound to DNA and the effect of restricted rotation on FRET are presented in this thesis. This thesis involves studying fluorophore photophysics in various microenvironments and then expanding into the solution stability and dynamics of the DNA sliding clamps.
ContributorsRanjit, Suman (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013