Matching Items (1,021)
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 dissertation, remote plasma interactions with the surfaces of low-k interlayer dielectric (ILD), Cu and Cu adhesion layers are investigated. The first part of the study focuses on the simultaneous plasma treatment of ILD and chemical mechanical polishing (CMP) Cu surfaces using N2/H2 plasma processes. H atoms and radicals in the plasma react with the carbon groups leading to carbon removal for the ILD films. Results indicate that an N2 plasma forms an amide-like layer on the surface which apparently leads to reduced carbon abstraction from an H2 plasma process. In addition, FTIR spectra indicate the formation of hydroxyl (Si-OH) groups following the plasma exposure. Increased temperature (380 °C) processing leads to a reduction of the hydroxyl group formation compared to ambient temperature processes, resulting in reduced changes of the dielectric constant. For CMP Cu surfaces, the carbonate contamination was removed by an H2 plasma process at elevated temperature while the C-C and C-H contamination was removed by an N2 plasma process at elevated temperature. The second part of this study examined oxide stability and cleaning of Ru surfaces as well as consequent Cu film thermal stability with the Ru layers. The ~2 monolayer native Ru oxide was reduced after H-plasma processing. The thermal stability or islanding of the Cu film on the Ru substrate was characterized by in-situ XPS. After plasma cleaning of the Ru adhesion layer, the deposited Cu exhibited full coverage. In contrast, for Cu deposition on the Ru native oxide substrate, Cu islanding was detected and was described in terms of grain boundary grooving and surface and interface energies. The thermal stability of 7 nm Ti, Pt and Ru ii interfacial adhesion layers between a Cu film (10 nm) and a Ta barrier layer (4 nm) have been investigated in the third part. The barrier properties and interfacial stability have been evaluated by Rutherford backscattering spectrometry (RBS). Atomic force microscopy (AFM) was used to measure the surfaces before and after annealing, and all the surfaces are relatively smooth excluding islanding or de-wetting phenomena as a cause of the instability. The RBS showed no discernible diffusion across the adhesion layer/Ta and Ta/Si interfaces which provides a stable underlying layer. For a Ti interfacial layer RBS indicates that during 400 °C annealing Ti interdiffuses through the Cu film and accumulates at the surface. For the Pt/Cu system Pt interdiffuion is detected which is less evident than Ti. Among the three adhesion layer candidates, Ru shows negligible diffusion into the Cu film indicating thermal stability at 400 °C.
ContributorsLiu, Xin (Author) / Nemanich, Robert (Thesis advisor) / Chamberlin, Ralph (Committee member) / Chen, Tingyong (Committee member) / Smith, David (Committee member) / Ponce, Fernando (Committee member) / Arizona State University (Publisher)
Created2012
Description
In this dissertation, the interface chemistry and electronic structure of plasma-enhanced atomic layer deposited (PEALD) dielectrics on GaN are investigated with x-ray and ultraviolet photoemission spectroscopy (XPS and UPS). Three interrelated issues are discussed in this study: (1) PEALD dielectric growth process optimization, (2) interface electronic structure of comparative PEALD dielectrics on GaN, and (3) interface electronic structure of PEALD dielectrics on Ga- and N-face GaN. The first study involved an in-depth case study of PEALD Al2O3 growth using dimethylaluminum isopropoxide, with a special focus on oxygen plasma effects. Saturated and self-limiting growth of Al2O3 films were obtained with an enhanced growth rate within the PEALD temperature window (25-220 ºC). The properties of Al2O3 deposited at various temperatures were characterized to better understand the relation between the growth parameters and film properties. In the second study, the interface electronic structures of PEALD dielectrics on Ga-face GaN films were measured. Five promising dielectrics (Al2O3, HfO2, SiO2, La2O3, and ZnO) with a range of band gap energies were chosen. Prior to dielectric growth, a combined wet chemical and in-situ H2/N2 plasma clean process was employed to remove the carbon contamination and prepare the surface for dielectric deposition. The surface band bending and band offsets were measured by XPS and UPS for dielectrics on GaN. The trends of the experimental band offsets on GaN were related to the dielectric band gap energies. In addition, the experimental band offsets were near the calculated values based on the charge neutrality level model. The third study focused on the effect of the polarization bound charge of the Ga- and N-face GaN on interface electronic structures. A surface pretreatment process consisting of a NH4OH wet chemical and an in-situ NH3 plasma treatment was applied to remove carbon contamination, retain monolayer oxygen coverage, and potentially passivate N-vacancy related defects. The surface band bending and polarization charge compensation of Ga- and N-face GaN were investigated. The surface band bending and band offsets were determined for Al2O3, HfO2, and SiO2 on Ga- and N-face GaN. Different dielectric thicknesses and post deposition processing were investigated to understand process related defect formation and/or reduction.
ContributorsYang, Jialing (Author) / Nemanich, Robert J (Thesis advisor) / Chen, Tingyong (Committee member) / Peng, Xihong (Committee member) / Ponce, Fernando (Committee member) / Smith, David (Committee member) / Arizona State University (Publisher)
Created2014
Description
This dissertation presents research findings on the three materials systems: lateral Si nanowires (SiNW), In2Se3/Bi2Se3 heterostructures and graphene. The first part of the thesis was focused on the growth and characterization of lateral SiNW. Lateral here refers to wires growing along the plane of substrate; vertical NW on the other hand grow out of the plane of substrate. It was found, using the Au-seeded vapor – liquid – solid technique, that epitaxial single-crystal SiNW can be grown laterally along Si(111) substrates that have been miscut toward [11− 2]. The ratio of lateral-to-vertical NW was found to increase as the miscut angle increased and as disilane pressure and substrate temperature decreased. Based on this observation, growth parameters were identified whereby all of the deposited Au seeds formed lateral NW. Furthermore, the nanofaceted substrate guided the growth via a mechanism that involved pinning of the trijunction at the liquid/solid interface of the growing nanowire.
Next, the growth of selenide heterostructures was explored. Specifically, molecular beam epitaxy was utilized to grow In2Se3 and Bi2Se3 films on h-BN, highly oriented pyrolytic graphite and Si(111) substrates. Growth optimizations of In2Se3 and Bi2Se3 films were carried out by systematically varying the growth parameters. While the growth of these films was demonstrated on h-BN and HOPG surface, the majority of the effort was focused on growth on Si(111). Atomically flat terraces that extended laterally for several hundred nm, which were separated by single quintuple layer high steps characterized surface of the best In2Se3 films grown on Si(111). These In2Se3 films were suitable for subsequent high quality epitaxy of Bi2Se3 .
The last part of this dissertation was focused on a recently initiated and ongoing study of graphene growth on liquid metal surfaces. The initial part of the study comprised a successful modification of an existing growth system to accommodate graphene synthesis and process development for reproducible graphene growth. Graphene was grown on Cu, Au and AuCu alloys at varioua conditions. Preliminary results showed triangular features on the liquid part of the Cu metal surface. For Au, and AuCu alloys, hexagonal features were noticed both on the solid and liquid parts.
Next, the growth of selenide heterostructures was explored. Specifically, molecular beam epitaxy was utilized to grow In2Se3 and Bi2Se3 films on h-BN, highly oriented pyrolytic graphite and Si(111) substrates. Growth optimizations of In2Se3 and Bi2Se3 films were carried out by systematically varying the growth parameters. While the growth of these films was demonstrated on h-BN and HOPG surface, the majority of the effort was focused on growth on Si(111). Atomically flat terraces that extended laterally for several hundred nm, which were separated by single quintuple layer high steps characterized surface of the best In2Se3 films grown on Si(111). These In2Se3 films were suitable for subsequent high quality epitaxy of Bi2Se3 .
The last part of this dissertation was focused on a recently initiated and ongoing study of graphene growth on liquid metal surfaces. The initial part of the study comprised a successful modification of an existing growth system to accommodate graphene synthesis and process development for reproducible graphene growth. Graphene was grown on Cu, Au and AuCu alloys at varioua conditions. Preliminary results showed triangular features on the liquid part of the Cu metal surface. For Au, and AuCu alloys, hexagonal features were noticed both on the solid and liquid parts.
ContributorsRathi, Somilkumar J (Author) / Drucker, Jeffery (Thesis advisor) / Smith, David (Committee member) / Chen, Tingyong (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
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
Group III-nitride semiconductors have wide application in optoelectronic devices. Spontaneous and piezoelectric polarization effects have been found to be critical for electric and optical properties of group III-nitrides. In this dissertation, firstly, the crystal orientation dependence of the polarization is calculated and in-plane polarization is revealed. The in-plane polarization is sensitive to the lateral characteristic dimension determined by the microstructure. Specific semi-polar plane growth is suggested for reducing quantum-confined Stark effect. The macroscopic electrostatic field from the polarization discontinuity in the heterostructures is discussed, b ased on that, the band diagram of InGaN/GaN quantum well/barrier and AlGaN/GaN heterojunction is obtained from the self-consistent solution of Schrodinger and Poisson equations. New device design such as triangular quantum well with the quenched polarization field is proposed. Electron holography in the transmission electron microscopy is used to examine the electrostatic potential under polarization effects. The measured potential energy profiles of heterostructure are compared with the band simulation, and evidences of two-dimensional hole gas (2DHG) in a wurtzite AlGaN/ AlN/ GaN superlattice, as well as quasi two-dimensional electron gas (2DEG) in a zinc-blende AlGaN/GaN are found. The large polarization discontinuity of AlN/GaN is the main source of the 2DHG of wurtzite nitrides, while the impurity introduced during the growth of AlGaN layer provides the donor states that to a great extent balance the free electrons in zinc-blende nitrides. It is also found that the quasi-2DEG concentration in zinc-blende AlGaN/GaN is about one order of magnitude lower than the wurtzite AlGaN/GaN, due to the absence of polarization. Finally, the InAlN/GaN lattice-matched epitaxy, which ideally has a zero piezoelectric polarization and strong spontaneous polarization, is experimentally studied. The breakdown in compositional homogeneity is triggered by threading dislocations with a screw component propagating from the GaN underlayer, which tend to open up into V-grooves at a certain thickness of the InxAl1-xN layer. The V-grooves coalesce at 200 nm and are filled with material that exhibits a significant drop in indium content and a broad luminescence peak. The structural breakdown is due to heterogeneous nucleation and growth at the facets of the V-grooves.
ContributorsWei, Qiyuan (Author) / Ponce, Fernando A. (Thesis advisor) / Tsen, Kong-Thon (Committee member) / Shumway, John (Committee member) / Menéndez, Jose (Committee member) / Smith, David (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
Recently a new materials platform consisting of semiconductors grown on GaSb and InAs substrates with lattice constants close to 6.1 A was proposed by our group for various electronic and optoelectronic applications. This materials platform consists of both II-VI (MgZnCdHg)(SeTe) and III-V (InGaAl)(AsSb) compound semiconductors, which have direct bandgaps spanning the entire energy spectrum from far-IR (~0 eV) up to UV (~3.4 eV). The broad range of bandgaps and material properties make it very attractive for a wide range of applications in optoelectronics, such as solar cells, laser diodes, light emitting diodes, and photodetectors. Moreover, this novel materials system potentially offers unlimited degrees of freedom for integration of electronic and optoelectronic devices onto a single substrate while keeping the best possible materials quality with very low densities of misfit dislocations. This capability is not achievable with any other known lattice-matched semiconductors on any available substrate. In the 6.1-A materials system, the semiconductors ZnTe and GaSb are almost perfectly lattice-matched with a lattice mismatch of only 0.13%. Correspondingly, it is expected that high quality ZnTe/GaSb and GaSb/ZnTe heterostructures can be achieved with very few dislocations generated during growth. To fulfill the task, their MBE growth and material properties are carefully investigated. High quality ZnTe layers grown on various III-V substrates and GaSb grown on ZnTe are successfully achieved using MBE. It is also noticed that ZnTe and GaSb have a type-I band-edge alignment with large band offsets (delta_Ec=0.934 eV, delta_Ev=0.6 eV), which provides strong confinement for both electrons and holes. Furthermore, a large difference in refractive index is found between ZnTe and GaSb (2.7 and 3.9, respectively, at 0.7 eV), leading to excellent optical confinement of the guided optical modes in planar semiconductor lasers or distributed Bragg reflectors (DBR) for vertical-cavity surface-emitting lasers. Therefore, GaSb/ZnTe double-heterostructure and ZnTe/GaSb DBR structure are suitable for use in light emitting devices. In this thesis work, experimental demonstration of these structures with excellent structural and optical properties is reported. During the exploration on the properties of various ZnTe heterostructures, it is found that residual tensile strains exist in the thick ZnTe epilayers when they are grown on GaAs, InP, InAs and GaSb substrates. The presence of tensile strains is due to the difference in thermal expansion coefficients between the epilayers and the substrates. The defect densities in these ZnTe layers become lower as the ZnTe layer thickness increases. Growth of high quality GaSb on ZnTe can be achieved using a temperature ramp during growth. The influence of temperature ramps with different ramping rates in the optical properties of GaSb layer is studied, and the samples grown with a temperature ramp from 360 to 470 C at a rate of 33 C/min show the narrowest bound exciton emission peak with a full width at half maximum of 15 meV. ZnTe/GaSb DBR structures show excellent reflectivity properties in the mid-infrared range. A peak reflectance of 99% with a wide stopband of 480 nm centered at 2.5 um is measured from a ZnTe/GaSb DBR sample of only 7 quarter-wavelength pairs.
ContributorsFan, Jin (Author) / Zhang, Yong-Hang (Thesis advisor) / Smith, David (Committee member) / Yu, Hongbin (Committee member) / Menéndez, Jose (Committee member) / Johnson, Shane (Committee member) / Arizona State University (Publisher)
Created2012