Matching Items (33)
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- All Subjects: Physics
- All Subjects: Astronomy
- Creators: Lindsay, Stuart
- Creators: Young, Patrick
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
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
A significant portion of stars occur as binary systems, in which two stellar components orbit a common center of mass. As the number of known exoplanet systems continues to grow, some binary systems are now known to harbor planets around one or both stellar components. As a first look into composition of these planetary systems, I investigate the chemical compositions of 4 binary star systems, each of which is known to contain at least one planet. Stars are known to vary significantly in their composition, and their overall metallicity (represented by iron abundance, [Fe/H]) has been shown to correlate with the likelihood of hosting a planetary system. Furthermore, the detailed chemical composition of a system can give insight into the possible properties of the system's known exoplanets. Using high-resolution spectra, I quantify the abundances of up to 28 elements in each stellar component of the binary systems 16 Cyg, 83 Leo, HD 109749, and HD 195019. A direct comparison is made between each star and its binary companion to give a differential composition for each system. For each star, a comparison of elemental abundance vs. condensation temperature is made, which may be a good diagnostic of refractory-rich terrestrial planets in a system. The elemental ratios C/O and Mg/Si, crucial in determining the atmospheric composition and mineralogy of planets, are calculated and discussed for each star. Finally, the compositions and diagnostics of each binary system are discussed in terms of the known planetary and stellar parameters for each system.
ContributorsCarande, Bryce (Author) / Young, Patrick (Thesis advisor) / Patience, Jennifer L (Thesis advisor) / Anbar, Ariel D (Committee member) / Arizona State University (Publisher)
Created2013
Description
Understanding the properties and formation histories of individual stars in galaxies remains one of the most important areas in astrophysics. The impact of the Hubble Space Telescope<\italic> (HST<\italic>) has been revolutionary, providing deep observations of nearby galaxies at high resolution and unprecedented sensitivity over a wavelength range from near-ultraviolet to near-infrared. In this study, I use deep HST<\italic> imaging observations of three nearby star-forming galaxies (M83, NGC 4214, and CGCG 269-049) based on the HST<\italic> observations, in order to provide to construct color-magnitude and color-color diagrams of their resolved stellar populations. First, I select 50 regions in the spiral arm and inter-arm areas of M83, and determine the age distribution of the luminous stellar populations in each region. I developed an innovative method of star-by-star correction for internal extinction to improve stellar age and mass estimates. I compare the extinction-corrected ages of the 50 regions with those determined from several independent methods. The young stars are much more likely to be found in concentrated aggregates along spiral arms, while older stars are more dispersed. These results are consistent with a scenario where star formation is associated with the spiral arms, and stars form primarily in star clusters before dispersing on short timescales to form the field population. I address the effects of spatial resolution on the measured colors, magnitudes, and age estimates. While individual stars can occasionally show measurable differences in the colors and magnitudes, the age estimates for entire regions are only slightly affected. The same procedure is applied to nearby starbursting dwarf NGC 4214 to study the distributions of young and old stellar populations. Lastly, I describe the analysis of the HST<\italic> and Spitzer Space Telescope<\italic> observations of the extremely metal-poor dwarf galaxy (XMPG) CGCG 269-049 at a distance of 4.96 Mpc. This galaxy is one of the most metal-poor known with 12+log(O/H)=7.43. I find clear evidence for the presence of an old stellar population in CGCG~269-049, ruling out the possibility that this galaxy is forming its first generation of stars, as originally proposed for XMPGs. This comprehensive study of resolved stellar populations in three nearby galaxies provides detailed view of the current state of star formation and evolution of galaxies.
ContributorsKim, Hwihyun (Author) / Windhorst, Rogier A (Thesis advisor) / Jansen, Rolf A (Committee member) / Rhoads, James E (Committee member) / Scannapieco, Evan (Committee member) / Young, Patrick (Committee member) / Arizona State University (Publisher)
Created2012
Description
After a decade of efforts, accurate and affordable DNA sequencing continues to remain an important goal in current research landscape. This thesis starts with a brief overview of the recent updates in the field of DNA sequencing technologies followed by description of the nanofluidics route to single molecule DNA detection. Chapter 2 presents discusses carbon nanotube(CNT) based nanofluidics. The fabrication and DNA sensing measurements of CNT forest membrane devices are presented. Chapter 3 gives the background for functionalization and recognition aspects of reader molecules. Chapter 4 marks the transition to solid state nanopore nanofluidics. The fabrication of Imidazole functionalized nanopores is discussed. The Single Molecule detection results of DNA from Palladium nanopore devices are presented next. Combining chemical recognition to nanopore technology, it has been possible to prolong the duration of single molecule events from the order of a few micro seconds to upto a few milliseconds. Overall, the work presented in this thesis promises longer single molecule detection time in a nanofludic set up and paves way for novel nanopore- tunnel junction devices that combine recognition chemistry, tunneling device and nanopore approach.
ContributorsKrishnakumar, Padmini (Author) / Lindsay, Stuart (Thesis advisor) / He, Jin (Committee member) / Vaiana, Sara (Committee member) / Schmidt, Kevin (Committee member) / Arizona State University (Publisher)
Created2013
Description
In this work, atomic force microscopy (AFM) and time resolved confocal fluorescence microscopy are combined to create a microscopy technique which allows for nanometer resolution topographic and fluorescence imaging. This technique can be applied to any sample which can be immobilized on a surface and which can be observed by fluorescence microscopy. Biological problems include small molecular systems, such as membrane receptor clusters, where very high optical resolutions need to be achieved. In materials science, fluorescent nanoparticles or other optically active nanostructures can be investigated using this technique. In the past decades, multiple techniques have been developed that yield high resolution optical images. Multiple far-field techniques have overcome the diffraction limit and allow fluorescence imaging with resolutions of few tens of nanometers. On the other hand, near-field microscopy, that makes use of optically active structures much smaller than the diffraction limit can give resolutions around ten nanometers with the possibility to collect topographic information from flat samples. The technique presented in this work reaches resolutions in the nanometer range along with topographic information from the sample. DNA origami with fluorophores attached to it was used to show this high resolution. The fluorophores with 21 nm distance could be resolved and their position on the origami determined within 10 nm. Not only did this work reach a new record in optical resolution in near-field microscopy (5 nm resolution in air and in water), it also gave an insight into the physics that happens between a fluorescent molecule and a dielectric nanostructure, which the AFM tip is. The experiments with silicon tips made a detailed comparison with models possible on the single molecule level, highly resolved in space and time. On the other hand, using silicon nitride and quartz as tip materials showed that effects beyond the established models play a role when the molecule is directly under the AFM tip, where quenching of up to 5 times more efficient than predicted by the model was found.
ContributorsSchulz, Olaf (Author) / Ros, Robert (Thesis advisor) / Levitus, Marcia (Committee member) / Liu, Yan (Committee member) / Lindsay, Stuart (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2012
Description
The only elements that were made in significant quantity during the Big Bang were hydrogen and helium, and to a lesser extent lithium. Depending on the initial mass of a star, it may eject some or all of the unique, newly formed elements into the interstellar medium. The enriched gas later collapses into new stars, which are able to form heavier elements due to the presence of the new elements. When we observe the abundances in a stellar regions, we are able to glean the astrophysical phenomena that occurred prior to its formation. I compile spectroscopic abundance data from 49 literature sources for 46 elements across 2836 stars in the solar neighborhood, within 150 pc of the Sun, to produce the Hypatia Catalog. I analyze the variability of the spread in abundance measurements reported for the same star by different surveys, the corresponding stellar atmosphere parameters adopted by various abundance determination methods, and the effect of normalizing all abundances to the same solar scale. The resulting abundance ratios [X/Fe] as a function of [Fe/H] are consistent with stellar nucleosynthetic processes and known Galactic thin-disk trends. I analyze the element abundances for 204 known exoplanet host-stars. In general, I find that exoplanet host-stars are not enriched more than the surrounding population of stars, with the exception of iron. I examine the stellar abundances with respect to both stellar and planetary physical properties, such as orbital period, eccentricity, planetary mass, stellar mass, and stellar color. My data confirms that exoplanet hosts are enriched in [Fe/H] but not in the refractory elements, per the self-enrichment theory for stellar composition. Lastly, I apply the Hypatia Catalog to the Catalog of Potentially Habitable Stellar Systems in order to investigate the abundances in the 1224 overlapping stars. By looking at stars similar to the Sun with respect to six bio-essential elements, I created maps that have located two ``habitability windows'' on the sky: (20.6hr, -4.8deg) and (22.6hr, -48.5deg). These windows may be of use in future targeted or beamed searches.
ContributorsHinkel, Natalie R (Author) / Timmes, Frank X (Thesis advisor) / Anbar, Ariel (Committee member) / Patience, Jennifer (Committee member) / Shumway, John (Committee member) / Young, Patrick (Committee member) / Arizona State University (Publisher)
Created2012
Description
Single molecules in a tunnel junction can now be interrogated reliably using chemically-functionalized electrodes. Monitoring stochastic bonding fluctuations between a ligand bound to one electrode and its target bound to a second electrode ("tethered molecule-pair" configuration) gives insight into the nature of the intermolecular bonding at a single molecule-pair level, and defines the requirements for reproducible tunneling data. Importantly, at large tunnel gaps, there exists a regime for many molecules in which the tunneling is influenced more by the chemical identity of the molecules than by variability in the molecule-metal contact. Functionalizing a pair of electrodes with recognition reagents (the "free analyte" configuration) can generate a distinct tunneling signal when an analyte molecule is trapped in the gap. This opens up a new interface between chemistry and electronics with immediate implications for rapid sequencing of single DNA molecules.
ContributorsChang, Shuai (Author) / Lindsay, Stuart (Thesis advisor) / Ros, Robert (Committee member) / Zhang, Peiming (Committee member) / Tao, Nongjian (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2012
Description
CpG methylation is an essential requirement for the normal development of mammals, but aberrant changes in the methylation can lead to tumor progression and cancer. An in-depth understanding of this phenomenon can provide insights into the mechanism of gene repression. We present a study comparing methylated DNA and normal DNA wrt its persistence length and contour length. Although, previous experiments and studies show no difference between the physical properties of the two, the data collected and interpreted here gives a different picture to the methylation phenomena and its effect on gene silencing. The study was extended to the artificially reconstituted chromatin and its interactions with the methyl CpG binding proteins were also probed.
ContributorsKaur, Parminder (Author) / Lindsay, Stuart (Thesis advisor) / Ros, Robert (Committee member) / Tao, Nongjian (Committee member) / Vaiana, Sara (Committee member) / Beckenstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2012