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QDs are mesoscopic objects with 3D quantum confinement, which are often called artificial atoms due to their discrete energy levels. Over the past several decades, a tremendous amount of research has been done on semiconductor QDs, which made them one of the most well-studied QD systems and a testbed for studying rich quantum phenomena that can be hosted in QD systems. But more recently, a new type of QD that is based on atomically thin graphene materials attracted the attention of the condensed matter physics community because of the unique electronic structures hosted by graphene materials. Compared to conventional semiconductor QDs, graphene QDs offer a distinctive platform to study the interplay between quantum confinement, relativistic quantum phenomena, and non-trivial band geometrical properties. Such properties cannot be investigated in conventional semiconductor QDs. During my Ph.D. study, my research focused on investigating the electronic structure and magnetic field response of these relatively new graphene QDs. To experimentally probe graphene QD states, I used an unconventional but very powerful in-situ graphene QD creation and probing technique with STM, which enabled us to gain information of graphene QD states with atomic scale spatial resolution and meV energy resolution. Such capability of our experimental approach enabled us to gain insights on graphene QD states that are out of reach with conventional electron transport measurements. In this dissertation, I will include experimental findings from four graphene QD projects that I participated in during my Ph.D. study. This includes the observation of giant orbital magnetic moments and paramagnetic shift in MLG QDs due to their relativistic nature (chapter 5), the effect of Berry curvature and Fermi surface symmetry on the spatial distribution of BLG QD wavefunctions (chapter 6), giant valley Zeeman splitting in TLG QDs due to the giant topological orbital magnetic moment hosted in this system (chapter 7), and the unambiguous direct visualization of the relativistic quantum scars in stadium shaped MLG QDs (chapter 8). These results demonstrate that unique quantum phenomena can be achieved in graphene QDs due to the interplay between quantum confinement, relativistic quantum phenomena, and non-trivial band geometrical properties.

Ultra-Fast Scanning Tunneling Microscopy (UFSTM) is a novel imaging technique that uses high intensity femtosecond laser light to generate atomic defect states called "traps" and provide subsequent atomic surface imaging between pulses. Many surface engineering applications are possible through femtosecond laser induced damage (fs-LID), a process where a strong non-perturbing laser electric field generates a high density of charge carriers that eventually thermalize and impart energy into a material's lattice changing the surface morphology. The number of pulses during illumination plays a large role in the resulting morphology with current theory predicting the formation of trap states in-between pulses. The trap states are too subtle to observe using traditional methods (ie. scanning electron microscopy or optical based microscopy). This thesis presents a coordinated effort in developing a novel scanning tunneling microscope system capable of detecting atomic trap states. In particular, a discussion of the instrumentation challenges associated with UFSTM techniques are presented. This work also includes a brief summary of the X-ray STM imaging technique that can also be used for elemental resolved surface imaging. The instrumentation challenges associated with coupling x-ray light with a standard STM system is included.

Abstract: Advancements in scanning tunneling microscopy (STM) have enabled atomic-scale lithographic patterning of logic gates, memory, and wires, by selectively passivating hydrogen (H) atoms on a H-terminated silicon (Si) surface. However, atomically fabricated systems encounter challenges of developing from research labs into commercial applications. This thesis focuses on developing a complementary metal-oxide semiconductor (CMOS) compatible process flow to nanofabricate a device capable of injecting and making signal measurements between CMOS and atomic circuitry; a macro-to-atom device. The design of the macro-to-atom device is capable of withstanding the high-temperature flashing required to prepare an area of H-terminated Si. By isolating the high-temperature flashing to a small area at the center of the device, damage to any prefabricated CMOS circuitry can be prevented. An initial design utilized tungsten-silicide (W-Si) conduction lines on a heavily-doped Si substrate to connect between the atomic and CMOS circuitry. However, the high-temperature surface preparation caused metal particulates to contaminate the center region where atomic circuitry would be fabricated, which could impede atomic circuit functionality. The high-temperature surface preparation also caused thin conduction lines to coagulate causing discontinuities. Another disadvantage to the initial device was that deposited W-Si on the Si surface increases the risk of STM tip crashing, as the surface is no longer flat. This would also make patterning continuous DB wires closely connecting to the W-Si conduction wires difficult. To circumvent these issues, a device using heavily-doped arsenic (As) conduction lines on a lightly-doped silicon substrate is to be utilized instead. Fabrication and testing of the device has been separated into three individual components to isolate and address development issues. The first component focuses on the main design and nanofabrication process flow of the bulk of the macro-to-atom device, and ensuring the process flow remains contaminant free. The second component focuses on the contact junctions that would directly interface with the atomic circuitry. By patterning atomic circuitry between the junctions, transport measurements are enabled that help further understand how the conductive contacts interact with the atomic circuitry and perturb the transmission spectra. The third component focuses on implanting a heavily-doped antimony (Sb) reservoir under the surface where atomic-scale lithography would occur, to provide the STM with the required carriers for low temperature operation and surface dangling bonds (DBs) with the required charge state. Once all components of the device are further realized, the three components can then be implemented together as a single macro-to-atom device.

The integer quantum Hall effect (IQH) demonstrates the robust quantization of longitudinal conductance of a 2D electron gas under a strong magnetic field. The theoretically predicted quantum anomalous Hall effect (QAH), which is the IQH counterpart with ferromagnetism taking the role of an external magnetic field, was experimentally demonstrated in 2013 in Cr doped (Bi_xSb_x)_2Te_3 (BST). However, the onset temperature (30 mK) is 2 orders of magnitude lower than the characteristic ferromagnetic critical temperature. The picture often used to describe QAH is this: a 2D topological surface state (SS) exists between the bulk conduction and valence bands. A Dirac mass gap opens when magnetic dopants e.g. Cr are added to create ferromagnetism. Due to its topological nature, a chiral edge state appears when the Fermi level is tuned into the mass gap. Using millikelvin visualization of SS Landau levels, we probe the spatial heterogeneity of the electronic structure due to Sb and Bi intercalation in both BST and CBST, hence discovering that Bi atoms cause a strong shift in the SS Dirac point which is independent of the disordered mass gap caused by the Cr atoms. In consequence, the electrostatic disorder randomizing the Dirac energy and magnetic disorder independently randomizing the Dirac mass gap conspire to drastically suppress the minimum energy gap into the range below 100 micro-eV for nanoscale regions separated by less than a micron. Thus our study reveals what fundamentally limits the fully quantized anomalous Hall effect in Sb2Te3-based ferromagnetic topological insulator (FMTI) materials to very low temperatures.

This dissertation is divided into two segments, both of which focus on creating and manipulating one-dimensional (1D) conduction channels in novel 1D and two-dimensional (2D) systems, characterized by scanning tunneling microscopy (STM).The first half describes how the electronic properties of quasi-1D graphene nanoribbons (GNRs) are manipulated by controlling their width and edge geometry at the atomic scale. A bottom-up approach is used for fabricating three different armchair GNR (AGNR) systems, allowing the geometry and hence the electronic properties of resultant AGNRs to be controlled. Successful molecular bandgap engineering in 1D AGNR heterojunctions is described, as well as the electronic and topographic characterization of the concentration dependence of boron-doped AGNRs. The discovery of two new in-gap dopant states with different symmetry is described. The successful fabrication and characterization of S-AGNRs having sulfur atoms substitutionally doped at the AGNR edges is also described. Our results indicate that S-doping induces a rigid shift of the energies for both the valence and conduction bands.The second half of this thesis describes how the 1T’ phase of monolayer transition metal dichalcogenides (TMDs) can be used as a platform to create 2D topological insulators (TIs). These novel TI systems are characterized in great detail. The successful growth and characterization of single-layer 1T’–WTe2 is described. This material is shown to host a bulk bandgap and helical edge states at the 1T’–vacuum interface. The growth and characterization of mixed phase-WSe2 is described. New techniques for creation and manipulation of edge conduction channels at interfaces between materials of different topologies are described.

Inelastic Electron Tunneling Spectroscopy with the Scanning Tunneling Microscope (STM-IETS) is a powerful technique used to characterize vibration and spin at the single molecule level. While IETS lacks hard selection rules, historically it has been assumed that vibrational overtones are rarely seen or even absent. Here we provide direct experimental evidence that the hindered rotation overtone excitation of CO molecules on Ag(110) can be detected with STM-IETS by isotope substitution. We also show that the anharmonicity of the overtone excitation can be characterized and compared between unique adsorption sites, and find evidence of anisotropy in the vibrational anharmonicity for CO adsorbed on the [1 1 0] step edge.

With evidence ranging from visual representations by scanning tunneling microscopes to the fluid and dynamic language of poetry, my research shows that we are shifting from a culture primarily based on ‘sight’ to one that is involved with ‘touch,’ metaphorically and literally speaking. Recent developments in theory and technology, especially quantum physics and post-structuralism, have redefined representation to encompass the necessary reflex of the representer. To be sure, my research has also found feminist and postcolonial criticisms to echo this theory: both have sought to challenge representations due to the objectivity normally attributed to the representer, the Cartesian logic of which quantum theory has destabilized. Thus, by reading poetry with a quantum theoretical lens, specifically the works of Gertrude Stein, Marianne Moore, Anne Carson, and Theresa Hak Kyung Cha, I show how ‘touch’ plays into our language, consequently affecting how we think through language.

The goal of the studies presented in this dissertation is to continuously expand the capability of a scanning tunneling microscope (STM) by improving its chemical sensitivity and temporal resolution. It has been demonstrated that the combination of STM with other techniques gains insight into the physical and chemical properties of single molecules. Single molecule rotational spectroscopy and microscopy is demonstrated using STM inelastic tunneling spectroscopy (IETS). We conduct real-space measurements of rotational transitions of gaseous hydrogen molecules physisorbed on surfaces at 10 K. The j=0 to j=2 rotational transition for para-H2 and HD were observed by STM-IETS. It is also found that the rotational energy is very sensitive to its local environment, we could precisely investigate how the environmental coupling modifies the structure, including the bond length, of a single molecule with sub-Ångström resolution. Due to this high sensitivity, the spatial variation in the potential energy surface can be quantified by the rotational and vibrational energies of the trapped H2. The ability of the tip to drag along a hydrogen molecule as it scans over another adsorbed molecule combined with the sensitivity of the hydrogen rotational excitation recorded by IETS to its immediate environment lead to the implementation of rotational spectromicroscopy, which helps us reveal the intermolecular interaction and charge transfer between H2 and a large molecule. Furthermore, we demonstrate that the H2 in the STM junction can be dissociated by the mechanical motion of the STM tip. Hydrogen rotational spectroscopy and microscopy provides novels approach toward visualizing and quantifying the local potential energy surface as well as the potential landscape of chemical reactions.Joint Ångström-femtosecond resolution is achieved by the combination of an STM with a femtosecond laser. We demonstrate the bond-selected, photo-assisted activation of a single C-H bond in an azulene molecule adsorbed on a Ag(110) surface. When the junction is illuminated by femtosecond laser, the electrons in the tip can be photo-excited into higher energy states and dissociate the molecule through a photo-assisted tunneling process. The photon-electron coupling at the junction enables the investigation of coherence molecular transformation with joint fs-Å resolution. We also show the band bending and laser induced band flattening at a molecule-semiconductor interface. More importantly, we observe the photo-induced, reversible conformational change between two structures for a single pyrrolidine molecule on a Cu(001) surface. The conductance changes of the STM junction associated with the structural transitions exhibits oscillates in time with periods corresponding to specific molecular vibrations. The vibrational frequencies and decay time are observed in real-space and real-time. Our laser-STM technique enables the investigation of inhomogeneous environmental effect on the molecular dynamics. We have found that the intermolecular interaction between two pyrrolidine molecules can increase the vibrational period while shortening its decay time. We anticipate that this novel technique would lead to a broad impact in physics and chemistry through direct visualization of coherently driven reactions resolved in space and time.

This dissertation discusses the theoretical basis and experimental applications to improving the capability of the STM in chemical and optical sensitivity. Traditional STM methods have achieved unprecedented spatial resolution, but suffer from a lack of sensitivity to chemical structure and composition. A new method of imaging, based on inelastic electron tunneling spectroscopy (IETS) measurement of hydrogen molecules is developed. The interaction of plasmon excitations to electronic states of a metal nano-cluster is also studied, allowing for better understanding of the mechanisms involved in the plasmon – electron coupling. Since its application at the single molecule level in the STM was realized, IETS has been used to identify different molecules through their vibrational signal. In recent experiments, rotational excitation of H2 was detected on metal and insulator surfaces. It was found that the energy of these excitations depend sensitively on the local chemical environment. By monitoring the rotational and vibrational IETS signal of the H2 across the molecule, a more chemically sensitive image can be constructed. When the method is applied to imaging magnesium porphyrin (MgP) on Au (110), different components of the molecule can be observed at different energies. These differences are indication of how the various components interact with the H2. Optical sensitivity of the STM manifests in the detection of photons emitted from the tunnel junction. Previous experiments have shown that we can map the excitation of molecular fluorescence with sub-Angstrom resolution. For applications in photochemistry and catalysis, understanding how plasmons interact with photons and electrons is crucial. Light emission from Au nanoclusters on oxide shows strong correlation with their electronic states. The interaction between plasmon mode in the junction and electronic states of the nano-clusters is further studied through clusters of different sizes and dimers. Emission of light from molecular orbitals is also investigated in panhematin and azulene molecules. Coupling of molecular orbital and vibronic states to junction plasmon is found and visualized through light emission spectrum and imaging.

Compared to intramolecular interactions, intermolecular interactions are relatively weak but they lay the foundation for research involving molecular recognition, self-assembly and surface adsorption in chemical and physical systems. This dissertation describes three different experimental approaches based on the detection of molecular vibrations to provide direct insights into intermolecular interactions at the sub-Ångström spatial resolution with a home built sub-Kelvin scanning tunneling microscope (STM).First, the intermolecular interaction can be evaluated by measuring the coupled vibrational mode of two interacting molecules with STM inelastic electron tunneling spectroscopy (IETS). The measurement of intermolecular coupled vibrations with tunable vertical and lateral displacements offers a direct assessment of the short range intermolecular repulsion in three dimensions.Second, the self-assembled molecular bonding structures can be imaged by the inelastic tunneling probe (itProbe). In itProbe, a carbon monoxide (CO) molecule is transferred onto the STM tip. The hindered translation energy of the CO-tip varies when it is positioned over different locations of the self-assembled structures. By recording the intensity variations of the inelastic electron tunneling signal caused by the energy shift, the geometric structure of each molecule and intermolecular interactions can be imaged in real space.Third, a sample surface can be considered as a giant molecule with infinite mass, and the binding strength of an adsorbed molecule on the surface is reflected in the external vibrations. The combination of the itProbe and IETS enable the determination of the adsorption configuration and low energy external vibrational modes of individual physisorbed benzene on an inert metal for the first time.All the approaches mentioned above rely on resolving fine spectral features induced by intermolecular interactions. The unprecedented spectral sensitivity, energy resolution and thermal stability achieved in 600 mK create the opportunity to study these weak intermolecular interaction effects at the single molecule level, which are otherwise obscured at higher temperatures.

Electrons show unusual and interesting behaviors both in low dimensions and on material surfaces, distinct from what they display in bulk materials. These intriguing properties have been studied in order to understand their origins. One area where this can be seen is in the case of superconductivity, where superconducting phase fluctuation in a thin superconductor is supposed to substantially suppress the superconductivity of the material as the film thickness decreases. To test this, we prepared epitaxially grown and globally flat lead (Pb) films; here, the thinnest film was 1.4 nm thick. Four different length scale measurements, ranging from the nm to the mm scale, gave consistent superconducting transition temperatures. Our results proved that the film of 1.4 nm still has strong superconducting phase stiffness; namely, the superfluid phase is rigid even in 1.4 nm thin superconductor film. Moreover, the parallel critical magnetic field is remarkably strong so that superconductivity is still observed in Zeeman fields, exceeding the Pauli limit. In addition, the surface of 3D topological insulator has a novel quantum state induced by strong spin-orbit interaction. A number of material studies were conducted to find a surface dominated conduction topological insulator that has a large energy gap and a single Dirac cone. Moreover, it is necessary for the material to be stable against aging unlike most 3D topological insulators, such as Bi₂Se₃. Here, Bi₂Te₂Se and BiSbTeSe₂ were studied in terms of their structures, electronic properties, and aging effects on them. Scanning tunneling microscopy analysis attested that Bi₂Te₂Se is an order alloy, which has a slight randomness of 15 %, whereas BiSbTeSe₂ is a random alloy. Scanning tunneling spectroscopy on BiSbTeSe₂ confirmed that the Dirac point tends to stay around the Fermi level under the strong band structure change, induced by random structure. The most surprising observation was that BiSbTeSe₂ showed remarkable stability despite the rich composition of selenium (Se). Even after aging for seven days, the Fermi level and the Dirac point remained at almost the same level in bulk band gap. Both observations are very important for applications to utilize the exotic topological surface state.

The power of rotational spectroscopy has long been demonstrated in the frequency domain by microwave spectroscopy, but its application in real space has been limited. Using a scanning tunneling microscope (STM) and inelastic electron tunneling spectroscopy (IETS), we were able to conduct real-space measurements of rotational transitions of gaseous hydrogen molecules physisorbed on surfaces at 10 K. The j=0 to j=2 rotational transition for para-H2 and HD were observed by STM-IETS. It is also found that the rotational energy is very sensitive to its local environment, we could precisely investigate how the environmental coupling modifies the structure, including the bond length, of a single molecule with sub-Angstrom resolution. Due to this high sensitivity, the spatial variation in the potential energy surface can be quantified by the rotational and vibrational energies of the trapped H2. The ability of the tip to drag along a hydrogen molecule as it scans over another adsorbed molecule combined with the sensitivity of the hydrogen rotational excitation recorded by IETS to its immediate environment lead to the implementation of rotational spectromicroscopy. Hydrogen rotational spectroscopy and microscopy provides novels approach toward visualizing and quantifying the intermolecular interaction as well as the intermediate processes of chemical reactions.

Understanding electron transfer at the molecular level is crucial for the rational design and performance improvement of organic optoelectronics and photovoltaics. Scanning tunneling microscope (STM) enables measurement of electronic properties with atomic precision. Here, we introduce a custom-built, laser-assisted STM that integrates optical excitation into the tunneling junction. The evanescent field generated by rear-incident laser light excites surface adsorbates on gold films, enabling the detection of optically induced changes in tunneling current under ambient conditions. Thin and atomically flat Au films epitaxially grown on c-cut sapphire prisms provide both efficient optical coupling and long-term stability to monitor optical activities of molecular donor-acceptor heterojunctions isolated in two-dimensional matrices on the surface. Our method offers a versatile platform to elucidate the involvement of individual states that affect charge generation and separation in a C60-tethered 2,5-dithienylpyrrole triad, a molecular donor-acceptor heterojunction, and to correlate the particular molecular orientations and local environment with the measured photocurrent of the anthracene-terminated aromatic thiolates in the tunneling junction.When alkanethiolate self-assembled monolayers on Au{111} are exchanged with alkaneselenols from solution, replacement of thiolates by selenols is rapid and complete, and is well described by perimeter-dependent island growth kinetics. The monolayer structures change as selenolate coverage increases, from being epitaxial and consistent with the initial thiolate structure to being characteristic of selenolate monolayer structures. At room temperature and at positive sample bias in scanning tunneling microscopy, the selenolate-gold attachment is labile, and molecules exchange positions with neighboring thiolates. The scanning tunneling microscope probe can be used to induce these place-exchange reactions.

The Scanning Tunneling Microscope (STM) is well known as one of the best spatially resolved microscopes today. Due not only to its microscopic ability, but also to its capability to manipulate individual atoms or molecules, it has been used as a very powerful tool in furthering the miniaturization of nanodevices. In my thesis, molybdenum difulfide(MoS2) and its derivatives on Cu(111) at low temperature in ultra-high vacuum(UHV) conditions are systematically investigated using a home-built STM. By slightly changing the preparation methods, we can synthesize MoS2 monolayer, Mo2S3 monolayer or Mo6S6 nanowires. Density Functional Theory (DFT) calculations were also performed to support and interpret experimental results.

Transition metal oxides (TMO) have proven to exhibit novel properties such as high temperature superconductivity, magnetic ordering, charge and spin density waves, metal to insulator transitions and colossal magnetoresistance. Among these are a spin-orbit coupling (SOC) induced Mott insulator Sr2IrO4. The electric transport properties of this material remain finite even at cryogenic temperatures enabling its complex electronic structure to be investigated by a scanning tunneling microscope. At T = 77 K, we observed two features which represent the Mott gap with a value of 2D ~ 615 meV. Additionally an inelastic loss feature was observed inside this gap due to a single magnon excitation at an energy of ~ 125 meV. These features are consistent with similar measurements with other probes. In addition to these features, at T = 4.2 K lower energy features appear which are believed to be due to additional magnetic ordering. Another material that exhibits a unique physical behavior is the sliding charge density wave (CDW) material TaS3. It is a quasi-one dimensional material that forms long narrow ribbon shaped crystals. It exhibits anomalies including non-ohmic conductivity, a decrease in the Young’s modulus, a decrease in the shear modulus and voltage induced changes in the crystal’s overall length. In addition, we have observed the torsional piezo-like response, voltage induced torsional strain (VITS), in TaS3 which was first discovered by Pokrovskii et. al. in 2007. Our measurements were conducted with a helical resonator. The VITS response has a huge effective piezoelectric coefficient of ~ 104 cm/V. In addition we have concluded that the VITS is a very slow response with time constants of ~ 1 s near the CDW depinning threshold, that these time constants are dependent on the CDW current, and we suggest that the VITS is due to residual twists being initially present in the crystal.

In the scope of this master thesis, a home-made brass scanning tunneling microscope (STM) was machined, assembled and tested for its functionality. For this microscope, a new approach-technique was used which follows the design suggested by Pan. The difference to Pan's design is the use of piezoplates, instead of piezostacks. Hence, the approach is still based on the stick and slip motion, but it allows the microscope to be more compact. A new and simple electronic circuit, in order to control the approach, is presented and was put together. This circuit is based on mechanical relays, which provide a sufficient long time gap between the single moving steps, due to their mechanical functional principle. Subsequently the approach-technique and the scanning was successfully tested. Finally, first images of HOPG were taken under ambient conditions.

This dissertation investigates four diverse molecular systems using ultrahigh vacuum low-temperature scanning tunneling microscope (UHV-LT-STM) manipulation and spectroscopic techniques to understand the fundamental properties of future nanotechnology applications.The first system demonstrated an extensive and unusual redistribution of spin density of cobalt porphyrin (TBrPP-Co) molecules adsorbed on a Cu(111) surface. Here the Kondo temperature increased dramatically on the porphyrin macrocycle as compared to the cobalt atom location. This effect was confirmed by monitoring the Kondo temperature with differential conductance (dI/dV) tunneling spectroscopy and spectroscopic mapping. In particular, it was found that an interfacial charge-transfer process between the molecule and the surface led to a spin delocalization in the TBrPPCo molecule, and resulted in a higher Kondo resonance on the lobe than the center of the molecule.The next two aspects of the research focused on a molecular level investigation of two different charge-transfer (CT) systems, 6T/F4TCNQ and TCNQ/ Mn(C5(CH3)5)2 on Au (111) surface. In the former system, the formation of new hybrid molecular orbitals in the 6T/F4TCNQ complex in a lateral configuration was evident by STM imaging at different bias voltages and differential conductance spectra. The CT led to the shift of HOMO and LUMO orbitals in the complex with respect to the pure molecular orbitals. A voltage dependent resonance-tunneling scheme was used to demonstrate a molecular switch made of 6T/ F4TCNQ CT complexes. In the latter system, charge-transfer process in a vertical stacking configuration was investigated. The comparative tunneling spectroscopy between the Mn(C5(CH3)5)2/Au(111) and Mn(C5(CH3)5)2/TCNQ/Au(111)assemblies clearly revealed the shift of frontier molecular orbitals. This explained detailed charge transfer mechanism induced by the deposition of a single Mn(C5(CH3)5)2 molecule on TCNQ layer.The last part of the dissertation focused on 4Fc3SEt double-decker molecular rotors on Au(111) surface. A conformational change of the rotator part of the molecule was realized by inelastic tunneling electron excitation using the STM-tip and a single tunneling electron energy transfer caused the conformational changes of the molecule. Furthermore, Kondo resonance and vibrational features of the molecular rotors were also identified from scanning tunneling spectroscopy measurements.

We demonstrate the successful down-scaling of donor-based silicon quantum dot structures to the single donor limit. These planar devices are realized in ultra high vacuum (UHV) by means of scanning tunneling microscope (STM) based hydrogen lithography which – in combination with a gaseous dopant source and a thermal silicon source – allows for the patterning of highly-doped planar Si:P structures with sub-nm precision encapsulated in a single-crystal environment. We present advancements of the alignment strategy for patterning ex-situ metallic contacts and top gates over the buried dopant devices. Here, we use a hierarchical array of etched registration markers. A key feature of the alignment process is the controlled formation of atomically flat plateaus several hundred nanometers in diameter that allows the active region of the device to be patterned on a single atomic Si(100) plane at a precisely known position. We present a multiterminal Si:P quantum dot device in the many-electron regime. Coplanar regions of highly doped silicon are used to gate the quantum dot potential resulting in highly stable Coulomb blockade oscillations. We compare the use of these all epitaxial in-plane gates with conventional metallic surface gates and find superior stability of the former. We highlight the challenges of down-scaling within a planar architecture and show how capacitance modeling can be used to optimize the tunability of quantum dot devices. Based on these results, we demonstrate the fabrication of an in-plane gated few-donor quantum dot device which shows highly stable Coulomb blockade oscillations as well as a surprisingly dense excitation spectrum on the scale of 100 μeV. We explain how these low energy resonances arise from transport through valley-split states of the silicon quantum dot providing extensive effective mass calculations to support our findings. Finally, we describe how STM H-lithography can be used to incorporate individual impurities at precisely known positions within a gated device and demonstrate transport through a single phosphorus donor. We find a bulk-like charging energy as well as clear indications for bulk-like excited states. We highlight the potential of this technology to realize elementary building blocks for future donor-based quantum computation applications in silicon.

This dissertation work is focused on the study of two molecular electronic systems: (BETS)2GaCl4 and a Nanoscale Protein Molecular Wire. The detailed structural and electronic study of these systems was carried out using a custom built Ultra-High Vacuum Low Temperature Scanning Tunneling Microscope (UHV-LT-STM). The STM is capable of studying these systems with a spatial and energy resolution that has never been achieved before. λ-(BETS)2GaCl4 is a charge transfer superconductor in bulk crystals. Using a unique deposition procedure, a single sheet of the superconductor was formed on a Ag(111) metal surface. Molecular resolution imaging of the well ordered molecular layer revealed the exact arrangement of the molecules on the surface. The superconductivity of the layer was confirmed by scanning tunneling spectroscopy and spectroscopic mapping. The superconducting signal remained down to a chain of only four molecular pairs, which was only 3.5 nm long. The structure of the nanoscale protein molecular wire is revealed by high resolution STM imaging. Single proteins are imaged and individual amino acid side chains are resolved. Electronic and vibrational properties are explored using the spectroscopic capability of the STM. The STM images, in combination with high resolution vibrational spectroscopy, allow for the first direct sequencing of individual proteins. These two systems have unique properties that could be used as key components in the new class of Nano/Bio electronics. By developing a better understanding of the properties of these systems at the nanoscale, this PhD study answers questions about the electronic and structural properties of these systems and points towards their future electronic and bio-medical applications.

We mimic beta-carotene (β-carotene) environment in plant leaves by using Au(111) as a substrate and conduct single molecule level studies in ultra high vacuum at low substrate temperatures of 77 K and 4.2 K. The STM images and manipulations studies identify five mechanically stable beta-carotene conformations on this substrate, with two never before reported by experiments. We confirm beta-carotene single molecule switching and molecular wire functionality. The beta-carotene clusters are disordered and rich in conformations. Single molecule extraction and cluster manipulation experiments indicate that intermolecular interactions of beta-carotene on Au(111) are stronger than molecule-substrate interactions. The mixtures of beta-carotene and chlorophyll-a result in three regions of ordered self-assembled chlorophyll-a, mobile beta-carotene, and their disordered mixtures with a ratio of 43.6±7.8% to 56.4±10.1% (over 9 mixtures), respectively, with 56.0±10.1% of beta-carotene being trans, indicating beta-carotene preferential mixing with chlorophyll-a instead of its own beta-carotene clusters. The results of this dissertation provide information on single molecule level properties of beta-carotene for fundamental understanding as well as for applications in green nano-bio-technology, nano-medicine, molecular electronics, and energy harvesting.

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.

Nanomanufacturing is an active research area in academia and industry due to the ever-growing demands for precision surface modifications of thin films or substrates with nanoscale features. Conventional lithographic techniques face many challenges as they approach their fundamental limits. Consequently, new nanomanufacturing tools, fabrication techniques, and precision instruments are being explored and developed to meet these challenges. It has been hypothesized that direct-write nanolithography might be achieved by using a field-emitted electron beam for nanomachining. This dissertation moves this research one step closer by developing a precision instrument that can enable the integration of direct-write nanolithography by a field-emitted electron beam with dimensional metrology by scanning tunneling microscopy. First, field emission from two prospective electron sources, a carbon nanotube field emitter and a sharp tungsten field emitter, is characterized at distances ranging from sub-micrometer to a few micrometers. Also, the design and construction of a low thermal drift piezoelectric linear motor is described for tip-sample approach. Experiments indicate that: the step size is highly repeatable with a standard deviation of less than 1.2 nm and the thermal stability is better than 40 nm/◦C. Finally, the design and construction of the instrument are presented. Experiments indicate that: the instrument is operating properly in scanning tunneling microscope mode with a resolution of less than 2 Å.

This thesis describes the study of two diverse systems, a cluster of silver atoms, and individual silver and bromine atoms, deposited on a metallic single crystal Ag(111)substrate, in the domain of atomic and molecular manipulation techniques, using a custom-built ultrahigh vacuum low temperature scanning tunneling microscope. A cluster of silver atoms was created by a controlled tip-sample contact. Single atoms were extracted from the cluster by using STM tip induced lateral manipulation. To investigate the mechanism of extraction in detail, atom extraction was carried out for different values of manipulation voltage and current. The threshold distance to pull an atom out from the cluster was determined. The tip-cluster distance proved to be the governing factor for the atom extraction mechanism. Lateral manipulation of a metal atom, silver, and a halogen atom, bromine, was carried out on a silver substrate with a silver coated tip apex. Silver atoms were extracted from a cluster of atoms, and bromine atoms were extracted from a cobalt porphyrin molecule using tunneling electron-induced bond dissociation technique. The threshold distance necessary to manipulate the silver atom and the bromine atom was determined. The lateral manipulation signals provided a value of the angle made by the tip with the surface at the first jump of the atom during manipulation. The interaction energy curves for these atoms were calculated using density functional theory. From a combination of all these results, a numerical value of force was obtained. This force corresponds to the threshold force necessary to move a silver atom and a bromine atom on the surface. The values of force provide an insight into the ionic and metallic interactions on the surface at the single atom level. The manipulation capability of the scanning tunneling microscope to build nanostructures was demonstrated by constructing a parabolic corral using locally extracted atoms. Since the surface vacancies and defects created during construction can be sealed off with the atoms and clusters after construction, this procedure resembles an atomic scale analog of a macroscale construction site.

We have developed a scanning probe microscopy method for probing the local Seebeck coefficient of individual layers of a thin-film superlattice structure. Development of this method involved modifying an existing scanning tunneling microscope (STM) by inserting a relay switch to connect the STM tip and the sample to an electrometer for measuring the thermovoltage generated by the contact of the STM tip to the warm sample. This method was used to measure the local Seebeck coefficient in each of the 20 layers of a p-type AlAs/GaAs thin-film superlattice. The results show an enhancement of the Seebeck coefficient in the GaAs quantum well layers when compared to the measurement result on a thick GaAs buffer layer with the same doping concentration as in the quantum wells

An Ultra High Vacuum Low Temperature Scanning Tunneling Microscope (UHV_LT_STM) for singe atom manipulation on Molecular Beam Epitaxy (MBE) grown nitride semiconductor samples has been designed and constructed. The operational capability of this STM is demonstrated on Ag(111) and GaN (000ī) surfaces at 6K and 80 K. On Ag(111) surface, individual silver atoms are repositioned by manipulating with the STM-tip. Conductance tunneling spectroscopy data acquired on this surface confirms the surface state onset at -63 meV. STM images of GaN (000ī) surface at 6 K shows novel low temperature reconstructed structures. STM images of this surface at 80 K reveals coexistence of 3x3, 6x4 and 6x6 regions and low temperature reconstructed structures.

In this thesis a low temperature scanning tunneling microscope will be constructed to explore the possibilities of atomic manipulation. In doing so we need to gain an understanding of the quantum mechanical theory of STM operation, set up a complex architecture of specialized equipment to achieve UHV conditions within the STM, control the tip of the microscope through the design and construction of a low noise high voltage amplifier, and record data conclusively demonstrating the ability of the STM to resolve nanoscale surface structures, while more importantly manipulating atoms in a controlled fashion.

Using a variable temperature scanning tunneling microscope, we have studied several adsorbates on silicon surfaces. We have studied the adsorption characteristics of H2S on Si(111)-(7×7). H2S adsorbs dissociatively at sub-monolayer coverage, from 50 to 300 K, with HS bonded to an adatom and H bonded to a rest atom. The adsorption is site selective and the adsorption site preference is temperature dependent. At 50 K, the faulted center sites are most favored for adsorption, followed by unfaulted center sites, faulted corner sites, and unfaulted corner sites. As the temperature is increased, the differences between the faulted and unfaulted halves diminish, but the center sites remain more reactive than the corner sites. We present an explanation to account for the non-Langmuir kinetics involved in this system. We have induced and imaged the dissociation of HS and DS on Si(111)-(7×7). Individual HS (or DS) fragments can be dissociated with the STM at low temperatures without affecting neighboring adsorbates. Near room temperature (297 K) and above, DS dissociates thermally, with an activation barrier of 0.73 ± 0.15 eV. The activation barrier was calculated from atomistic studies of the dissociation rates at temperatures between 297 and 312 K. We have induced and imaged the dissociation of D2S on Si(100). D2S dissociates into DS and D below 200 K. Individual DS fragments can be dissociated with the STM at low temperatures. At 200 K or above, D2S dissociates into S and two D’s. D2S adsorption affects the surface reconstruction on Si(100), from the buckled dimer configuration to the dynamically flipping configuration and vice versa. We have studied the adsorption and STM induced desorption of NO from Si(111)-(7×7). NO adsorbs preferentially on faulted corner sites, followed by faulted center sites, unfaulted corner sites and unfaulted center sites. The preference for the different adsorption sites is independent of temperature and correlates well with the local density of states at these sites. NO can be desorbed from Si(111) by the STM. The data suggest the desorption is induced by the electric field under the STM tip. The threshold positive electric field for desorption of NO is 0.114 ± 0.009 V/°A.