Thesis (Ph.D.)--Hong Kong University of Science and Technology, 2007. / Vita. Includes bibliographical references (leaves 116-130). Also available in electronic version.

Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 183-190).

The electron transfer mechanisms of multiheme cytochromes were examined with scanning tunneling microscopy (STM). To simulate bacterial metal reduction mediated by proteins in direct contact with mineral surfaces, monolayers of purified decaheme cytochromes from the metal-reducing bacterium Shewanella oneidensis were prepared on Au(111) surfaces. Recombinant tetracysteine sequences were added to two outermembrane decaheme cytochromes (OmcA and MtrC) from S. oneidensis MR-1 to ensure chemical immobilization on Au(111). STM images of the cytochrome monolayers showed good coverage and their shapes/sizes matched that predicted by their respective molecular masses. Current-voltage (I-V) tunneling spectroscopy revealed that OmcA and MtrC exhibit characteristic tunneling spectra. Theoretical modeling of the single-molecule tunneling spectra revealed a distinct tunneling mechanism for each cytochrome: OmcA mediates tunneling current coherently whereas MtrC temporarily traps electrons via orbital-mediated tunneling. These mechanisms suggest a superexchange electron transfer mechanism for OmcA and a redox-specific (i.e. heme-mediated) electron transfer mechanism for MtrC at mineral surfaces during bacterial metal reduction. Additionally, a novel electrochemical STM configuration was designed to measure tunneling current from multiheme cytochromes to hematite (001) surfaces in various electrolyte solutions. Current-distance (I-s) profiles on hematite (001) reveal predictable electric double layer structure that changes with ionic strength. The addition of the small tetraheme cytochrome c (STC) from S. oneidensis on insulated Au tips resulted in modified tunneling profiles that suggest STC significantly modulates the double layer. This observation is relevant to understanding metal reduction in cases where terminal metal-reducing enzymes are unable to come in direct contact with reducible mineral surfaces. Electronic coupling to the mineral surface might therefore be mediated by a localized ion swarm specific to the mineral surface. / Ph. D.

Natural and synthetic SnO₂ samples were studied using scanning tunneling microscopy (STM). The SnO₂ surface flattens considerably following high temperature treatments up to 1500 K. The conductivity of the synthetic SnO₂ surface is significantly reduced following annealing at temperatures of approximately 1200-1500 K, making tunneling impossible. A decrease in conductivity was not observed for the natural SnO₂ sample following similar high temperature treatments, most likely due to impurities which act as dopants. No atomic scale images were collected on the SnO₂ surface which provided information regarding atomic positions and point defects on the surface. Water adsorption was studied on the stoichiometric Cr₂O₃ (101̲2) surface, using thermal desorption spectroscopy (TDS). Water was the only desorption product observed during TDS. Adsorption is primarily dissociative following exposure to water at 163 K. Approximately, 0.12 monolayers of water dissociate on the clean, nearly stoichiometric Cr₂O₃ (101̲2) surface. The first order kinetics observed for the recombination of dissociated water are not well understood. One possible explanation is that the rate limiting step for desorption involves the breaking of a Cr-O bond resulting in a freely diffusing OH species. The exchange of halogen and oxygen was studied on Cr₂O₃ (101̲2) using Auger electron spectroscopy (AES) and TDS. The exchange of chlorine and oxygen is completely reversible. Chlorine is removed from the Cr₂O₃ (101̲2) surface following exposure to oxygen. Exposure of CFCl₂CH₂Cl reduces the surface oxygen concentration to that of the clean, nearly stoichiometric Cr₂O₃ (101̲2) surface. The exchange of chlorine with oxygen appears to involve only chemisorbed surface oxygen, not bulk lattice oxygen. / Master of Science

Thesis advisor: Vidya Madhavan / Spin-orbit coupling (SOC) is the interaction of an electron's intrinsic angular momentum (spin) with its orbital momentum. The strength of this interaction is proportional to Z<super>4</super> where Z is the atomic number, so generally it is stronger in atoms with higher atomic number, such as bismuth (Z=83) and iridium (Z=77). In materials composed of such heavy elements, the prominent SOC can be sufficient to modify the band structure of the system and lead to distinct phase of matter. In recent years, SOC has been demonstrated to play a critical role in determining the unusual properties of a variety of compounds. SOC associated materials with exotic electronic states have also provided a fertile platform for studying emergent phenomena as well as new physics. As a consequence, the research on these interesting materials with any insight into understanding the microscopic origin of their unique properties and complex phases is of great importance. In this context, we implement scanning tunneling microscopy (STM) and spectroscopy (STS) to explore the surface states (SS) of the two major categories of SOC involved materials, Bi-based topological insulators (TI) and Ir-based transition metal oxides (TMO). As a powerful tool in surface science which has achieved great success in wide variety of material fields, STM/STS is ideal to study the local density of states of the subject material with nanometer length scales and is able to offer detailed information about the surface electronic structure. In the first part of this thesis, we report on the electronic band structures of three-dimensional TIs Bi₂Te₃ and Bi₂Se₃. Topological insulators are distinct quantum states of matter that have been intensely studied nowadays. Although they behave like ordinary insulators in showing fully gapped bulk bands, they host a topologically protected surface state consisting of two-dimensional massless Dirac fermions which exhibits metallic behavior. Indeed, this unique gapless surface state is a manifestation of the non-trivial topology of the bulk bands, which is recognized to own its existence to the strong SOC. In chapter 3, we utilize quasiparticle interference (QPI) approach to track the Dirac surface states on Bi₂Te₃ up to ~800 meV above the Dirac point. We discover a novel interference pattern at high energies, which probably originates from the impurity-induced spin-orbit scattering in this system that has not been experimentally detected to date. In chapter 4, we discuss the topological SS evolution in (Bi_1-xIn_x)₂Se₃ series, by applying Landau quantization approach to extract the band dispersions on the surface for samples with different indium content. We propose that a topological phase transition may occur in this system when x reaches around 5%, with the experimental signature indicating a possible formation of gapped Dirac cone for the surface state at this doping. In the second part of this thesis, we focus on investigating the electronic structure of the bilayer strontium iridate Sr₃Ir₂O₇. The correlated iridate compounds belong to another domain of SOC materials, where the electronic interaction is involved as well. Specifically, the unexpected Mott insulating state in 5<italic>d</italic>-TMO Sr₂IrO₄ and Sr₃Ir₂O₇ has been suggested originate from the cooperative interplay between the electronic correlations with the comparable SOC, and the latter is even considered as the driving force for the extraordinary ground state in these materials. In chapter 6, we carried out a comprehensive examination of the electronic phase transition from insulating to metallic in Sr₃Ir₂O₇ induced by chemical doping. We observe the subatomic feature close to the insulator-to-metal transition in response with doping different carriers, and provide detailed studies about the local effect of dopants at particular sites on the electronic properties of the system. Additionally, the basic experimental techniques are briefly described in chapter 1, and some background information of the subject materials are reviewed in chapter 2 and chapter 5, respectively. / Thesis (PhD) — Boston College, 2014. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Physics.

The electronic structures of Mn £_-doped epitaxial GaN films grown on sapphire substrates are studied by scanning tunneling microscopy in this work. Local structural information and the corresponding electronic properties of Mn £_-doped GaN films are probed by the combination of scanning tunneling microscopy and atomic-scale scanning tunneling spectroscopy measurements. According to the electronic local density of states analysis indicates that Mn ions develop an acceptor level in GaN, revealing a gap state located at ~ 1.4 eV above the valence band edge of GaN. Furthermore, the energy position of the charge transfer levels of substitutional MnGa within GaN energy gap is also elucidated and discussed in the work.

Superconductivity is a remarkable quantum phenomenon in which a macroscopic number of electrons form a condensate of Cooper pairs that can be described by a single quantum wave function. According to the celebrated Bardeen-Cooper-Schrieffer (BCS) theory of superconductivity, there is a minimum length scale (the coherence length) below which the condensate has a rigid quantum phase. The fate of superconductivity in a system with spatial dimensions smaller than [the coherence length] has been the subject of intense interest for decades and recent studies of superconductivity in ultra-thin epitaxial metal films have revealed some surprising behaviors in light of BCS theory. Notably, it was found that superconductivity remains robust in thin lead films with thicknesses orders of magnitude smaller than the coherence length (i.e. in the extreme two dimensional limit). Such studies raise the critical question: what happens to superconductivity as all dimensions are reduced toward the zero dimensional limit? By controlling the lateral size of ultra thin 2D islands, we systematically address this fundamental question with a detailed scanning tunneling microscopy/spectroscopy study. We show that as the lateral dimension is reduced, the strength of the superconducting order parameter is also reduced, at first slowly for dimensions larger than the bulk coherence length, and then dramatically at a critical length scale of ~ 40nm. We find this length scale corresponds to the lateral decay length of the order parameter in an island containing regions of different heights and different superconducting strength. Overall, our results suggest that fluctuation corrections to the BCS theory are important in our samples and may need to be systematically addressed by theory. / text

This research work is aimed at understanding the electronic properties of Bi(110) nanostructures. This study chiefly uses Scanning Tunneling Microscopy (STM), Scanning Tunneling Spectroscopy (STS) and Non Contact Atomic Force Microscope (NCAFM) to investigate the geometric and electronic structure of Bi(110) islands on highly oriented pyrolytic graphite (HOPG) substrate. STM measurements are the primary focus of the thesis which involves imaging the bismuth islands and study of its atomic structure. STM images of the Bi(110) islands reveal a ‘wedding cake’ profile of the bismuth islands that show paired layers on top of a base. I(V) (Current vs voltage) data was acquired via STS techniques and its first derivative was compared to DFT calculations. The comparison implied the presence of a dead wetting layer which was present only underneath the bismuth islands. We observed bilayer damped oscillations in the surface energy that were responsible for the stability of paired layers in Bi(110) islands. Interesting Moiré pattern arising out of misorientation between the substrate and the overlayer are also observed in STM images on some bismuth islands. Bright features pertaining to enhanced LDOS (local density of states) were observed on the perimeter of the bismuth islands and stripes in the STM images and STS dI/dV maps which appear at energies around the Fermi level. The bright features which we termed as ‘bright beaches (BB)’ are also observed on grain boundaries and defects that suggest that they are related to termination of the chain of bismuth atoms. The Bi(110) islands and stripes were observed to form preferred widths with a well defined periodicity. This peculiar phenomenon was attributed to a lateral quantum size effect (QSE) that results from a Fermi wave vector with appropriate shifts in Fermi energy. The widths of the islands prefer to adjust themselves at the nodes of this in-plane Fermi wavelength. NaCl deposited on a HOPG substrate forms cross shaped islands which were used as spacers to limit the interaction between the bismuth films and the underlying HOPG substrate. The NaCl islands are transparent to the flow of tunneling current and allow STS measurements. The LDOS of Bi/HOPG was very similar to the LDOS of Bi deposited on NaCl/HOPG which suggests that the wetting layer underneath the bismuth islands plays an important role in decoupling the film from the underlying substrate.

Organic electronics are becoming an increasingly important part of the semiconductor industry, with myriad applications enabled by their low cost, solution processability, and electrical conductivity. Charge transport in electronic applications involving organic semiconductor materials depends strongly on the electronic properties of nanoscale interfaces. Local variations in molecular environments can have a significant impact on the interfacial electronic properties, and subsequently the organic semiconductor electronic structure. Here, we use scanning tunneling microscopy and spectroscopy, supported by theoretical calculations, to investigate the impact of the local adsorption environment on the local density of states of oligothiophenes, carbon nanohoops, and carbon nanotubes. First, we present work showing that, for alkyl-substituted quaterthiophenes, molecular packing and electronic structure at interfaces differ substantially from the bulk, and a significant degree of structural and electronic variation occurs even in this relatively simple system. Then, we report on investigations of longer alkyl-substituted oligothiophenes, were we found a variety of planar molecular conformations that surprising exhibited similar, particle-in-a-box-like progressions of unoccupied molecular orbitals. Next, we share our research that found, for the first time, metal surface electrons confined within single adsorbed molecules. Finally, we study the impact of electrostatic defects in both metal and dielectric substrates on single-walled carbon nanotubes. The research presented in this dissertation increases our understanding of organic semiconductor interfaces and the impact of said interfaces on local molecular electronic structure, thereby aiding future organic semiconductor technological development. / 10000-01-01

This dissertation provides a brief introduction into scanning tunneling microscopy, and then Chapter III reports on the design and operation of a cryogenic ultra-high vacuum scanning tunneling microscope (STM) coupled to a closed-cycle cryostat (CCC). The STM is thermally linked to the CCC through helium exchange gas confined inside a volume enclosed by highly flexible rubber bellows. The STM is thus mechanically decoupled from the CCC, which results in a significant reduction of the mechanical noise transferred from the CCC to the STM. Noise analysis of the tunneling current shows current fluctuations up to 4% of the total current, which translates into tip-sample distance variations of up to 1.5 picometers. This noise level is sufficiently low for atomic-resolution imaging of a wide variety of surfaces. To demonstrate this, atomic-resolution images of Au(111) and NaCl(100)/Au(111) surfaces, as well as of carbon nanotubes deposited on Au(111), were obtained. Other performance characteristics such as thermal drift analysis and a cool-down analysis are reported. Scanning tunneling spectroscopy (STS) measurements based on the lock-in technique were also carried out and showed no detectable presence of noise from the CCC. These results demonstrate that the constructed CCC-coupled STM is a highly stable instrument capable of highly detailed spectroscopic investigations of materials and surfaces at the atomic-scale. A study of electron transport in single-walled carbon nanotubes (SWCNTs) was also conducted. In Chapter IV, STS is used to study the quantum-confined electronic states in SWCNTs deposited on the Au(111) surface. The STS spectra show the vibrational overtones which suggest rippling distortion and dimerization of carbon atoms on the SWCNT surface. This study experimentally connects the properties of well-defined localized electronic states to the properties of their associated vibronic states. In Chapter V, a study of PbS nanocrystals was conducted to study the effect of localized sub-bandgap states associated with surface imperfections. A correlation between their properties and the atomic-scale structure of chemical imperfections responsible for their appearance was established to understand the nature of such surface states. This dissertation includes both previously published/unpublished and co-authored material.