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- All Subjects: Physics
- Creators: Lindsay, Stuart
- Creators: Schmidt, Kevin
- Member of: Theses and Dissertations
- Member of: Barrett, The Honors College Thesis/Creative Project Collection
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
Single molecule identification is one essential application area of nanotechnology. The application areas including DNA sequencing, peptide sequencing, early disease detection and other industrial applications such as quantitative and quantitative analysis of impurities, etc. The recognition tunneling technique we have developed shows that after functionalization of the probe and substrate of a conventional Scanning Tunneling Microscope with recognition molecules ("tethered molecule-pair" configuration), analyte molecules trapped in the gap that is formed by probe and substrate will bond with the reagent molecules. The stochastic bond formation/breakage fluctuations give insight into the nature of the intermolecular bonding at a single molecule-pair level. The distinct time domain and frequency domain features of tunneling signals were extracted from raw signals of analytes such as amino acids and their enantiomers. The Support Vector Machine (a machine-learning method) was used to do classification and predication based on the signal features generated by analytes, giving over 90% accuracy of separation of up to seven analytes. This opens up a new interface between chemistry and electronics with immediate implications for rapid Peptide/DNA sequencing and molecule identification at single molecule level.
ContributorsZhao, Yanan, 1986- (Author) / Lindsay, Stuart (Thesis advisor) / Nemanich, Robert (Committee member) / Qing, Quan (Committee member) / Ros, Robert (Committee member) / Zhang, Peiming (Committee member) / Arizona State University (Publisher)
Created2014
Description
ABSTRACT
X-Ray crystallography and NMR are two major ways of achieving atomic
resolution of structure determination for macro biomolecules such as proteins. Recently, new developments of hard X-ray pulsed free electron laser XFEL opened up new possibilities to break the dilemma of radiation dose and spatial resolution in diffraction imaging by outrunning radiation damage with ultra high brightness femtosecond X-ray pulses, which is so short in time that the pulse terminates before atomic motion starts. A variety of experimental techniques for structure determination of macro biomolecules is now available including imaging of protein nanocrystals, single particles such as viruses, pump-probe experiments for time-resolved nanocrystallography, and snapshot wide- angle x-ray scattering (WAXS) from molecules in solution. However, due to the nature of the "diffract-then-destroy" process, each protein crystal would be destroyed once
probed. Hence a new sample delivery system is required to replenish the target crystal at a high rate. In this dissertation, the sample delivery systems for the application of XFELs to biomolecular imaging will be discussed and the severe challenges related to the delivering of macroscopic protein crystal in a stable controllable way with minimum waste of sample and maximum hit rate will be tackled with several different development of injector designs and approaches. New developments of the sample delivery system such as liquid mixing jet also opens up new experimental methods which gives opportunities to study of the chemical dynamics in biomolecules in a molecular structural level. The design and characterization of the system will be discussed along with future possible developments and applications. Finally, LCP injector will be discussed which is critical for the success in various applications.
X-Ray crystallography and NMR are two major ways of achieving atomic
resolution of structure determination for macro biomolecules such as proteins. Recently, new developments of hard X-ray pulsed free electron laser XFEL opened up new possibilities to break the dilemma of radiation dose and spatial resolution in diffraction imaging by outrunning radiation damage with ultra high brightness femtosecond X-ray pulses, which is so short in time that the pulse terminates before atomic motion starts. A variety of experimental techniques for structure determination of macro biomolecules is now available including imaging of protein nanocrystals, single particles such as viruses, pump-probe experiments for time-resolved nanocrystallography, and snapshot wide- angle x-ray scattering (WAXS) from molecules in solution. However, due to the nature of the "diffract-then-destroy" process, each protein crystal would be destroyed once
probed. Hence a new sample delivery system is required to replenish the target crystal at a high rate. In this dissertation, the sample delivery systems for the application of XFELs to biomolecular imaging will be discussed and the severe challenges related to the delivering of macroscopic protein crystal in a stable controllable way with minimum waste of sample and maximum hit rate will be tackled with several different development of injector designs and approaches. New developments of the sample delivery system such as liquid mixing jet also opens up new experimental methods which gives opportunities to study of the chemical dynamics in biomolecules in a molecular structural level. The design and characterization of the system will be discussed along with future possible developments and applications. Finally, LCP injector will be discussed which is critical for the success in various applications.
ContributorsWang, Dingjie (Author) / Spence, John CH (Thesis advisor) / Weierstall, Uwe (Committee member) / Schmidt, Kevin (Committee member) / Fromme, Petra (Committee member) / Ozkan, Banu (Committee member) / Arizona State University (Publisher)
Created2014
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
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
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
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
Quark matter at sufficiently high density and low temperature is expected to be a color superconductor, and may exist in the interior of neutron stars. The properties of two simplest possible color-superconducting phases, i.e., the color-flavor-locked (CFL) and two-flavor superconducting (2SC) phases, are reviewed. The effect of a magnetic field on the pairing dynamics in two-flavor color-superconducting dense quark matter is investigated. A universal form of the gap equation for an arbitrary magnetic field is derived in the weakly coupled regime of QCD at asymptotically high density, using the framework of Schwinger-Dyson equation in the improved rainbow approximation. The results for the gap in two limiting cases, weak and strong magnetic fields, are obtained and discussed. It is shown that the superconducting gap function in the weak magnetic field limit develops a directional dependence in momentum space. This property of the gap parameter is argued to be a consequence of a long-range interaction in QCD.
ContributorsYu, Lang (Author) / Shovkovy, Igor A. (Thesis advisor) / Lunardini, Cecilia (Committee member) / Schmidt, Kevin (Committee member) / Alarcon, Ricardo (Committee member) / Lebed, Richard (Committee member) / Arizona State University (Publisher)
Created2012
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
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