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 This dissertation includes both previously published/unpublished and co-authored material.

This dissertation presents results of a project bringing Scanning Tunneling Microscope (STM) into a regime of unlimited operational time at cryogenic conditions. Freedom from liquid helium consumption was achieved and technical characteristics of the instrument are reported, including record low noise for a scanning probe instrument coupled to a close-cycle cryostat, which allows for atomically resolved imaging, and record low thermal drift. Subsequent studies showed that the new STM opened new prospects in nanoscience research by enabling Scanning Tunneling Spectroscopic (STS) spatial mapping to reveal details of the electronic structure in real space for molecules and low-dimensional nanomaterials, for which this depth of investigation was previously prohibitively expensive. Quantum-confined electronic states were studied in single-walled carbon nanotubes (SWCNTs) deposited on the Au(111) surface. Localization on the nanometer-scale was discovered to produce a local vibronic manifold resulting from the localization-enhanced electron-vibrational coupling. STS showed the vibrational overtones, identified as D-band Kekulé vibrational modes and K-point transverse out-of plane phonons. This study experimentally connected the properties of well-defined localized electronic states to the properties of associated vibronic states. Electronic structures of alkyl-substituted oligothiophenes with different backbone lengths were studied and correlated with torsional conformations assumed on the Au(111) surface. The molecules adopted distinct planar conformations with alkyl ligands forming cis- or trans- mutual orientations and at higher coverage self-assembled into ordered structures, binding to each other via interdigitated alkyl ligands. STS maps visualized, in real space, particle-in-a-box-like molecular orbitals. Shorter quaterthiophenes have substantially varying orbital energies because of local variations in surface reactivity. Different conformers of longer oligothiophenes with significant geometrical distortions of the oligothiophene backbones surprisingly exhibited similar electronic structures, indicating insensitivity of interaction with the surface to molecular conformation. Electronic states for annealed ligand-free lead sulfide nanocrystals were investigated, as well as hydrogen-passivated silicon nanocrystals, supported on the Au(111) surface. Delocalized quantum-confined states and localized defect-related states were identified, for the first time, via STS spatial mapping. Physical mechanisms, involving surface reconstruction or single-atom defects, were proposed for surface state formation to explain the observed spatial behavior of the electronic density of states. This dissertation includes previously published co-authored material.

A series of para-substituted phenylethylamine analogues bound to the enzyme aromatic amine dehydrogenase have been simulated using quantum mechanical electronic structure calculations and molecular mechanical molecular dynamics simulations. Trends have been verified connecting bond dissociation energy (and thus driving force) to observed rate constants and activation enthalpy. Trends have been identified in connecting statistics drawn from molecular dynamics simulations and the temperature dependence of the kinetic isotope effect, notably that as the temperature dependence of the kinetic isotope effect increases the flexibility of the promoting vibration decreases. This is explained as being more effected by thermal energy put into the system, and therefore more affected by temperature.

The growth mechanism of chemical vapor deposition (CVD) grown homo-epitaxial diamond (110) and (111) films was studied using ultrahigh vacuum (UHV) scanning tunneling microscopy (STM). In addition, the field emission properties of diamond coated molybdenum microtips were studied as a function of exposure to different gases.

Thesis advisor: Ilija Zeljkovic / We used spectroscopic-imaging scanning tunneling microscopy (SI-STM) and spin-polarized STM (SP-STM) to unveil new electronic phenomena in several different quantum systems. We explored: (1) a potential topological superconductor heterostructure Bi₂Te₃/Fe(Te, Se), (2) high-Tc superconductors − Bi₂Sr₂CaCu₂O₈₊ₓ and Fe(Te, Se), and (3) doped spin-orbit Mott insulators Sr₂IrO₄ and Sr₃Ir₂O₇. In Bi₂Te₃/Fe(Te, Se), we observed superconductivity (SC) on the surface of Bi₂Te₃ thin film, induced by the iron-based superconductor substrate. By annealing the optimally-doped cuprate superconductor Bi₂Sr₂CaCu₂O₈₊ₓ, we drastically lowered the surface hole doping concentration to detect a unidirectional charge stripe order, the first reported charge order on an insulating (defined by the spectral gap with zero conductance spanning the Fermi level) cuprates surface. In the high-Tc SC Fe(Te, Se) single crystal, we found local regions of electronic nematicity, characterized by C₂ quasiparticle interference (QPI) induced by Fermi surface anisotropy and inequivalent spectral weight of dyz and dxz orbitals near Fermi level. Interestingly, the nematic order is locally strongly anti-correlated with superconductivity. Finally, utilizing SP-STM, we observed a short-range antiferromagnetic (AF) order near the insulator-metal transition (IMT) in spin-orbital Mott insulators Sr₂IrO₄ and Sr₃Ir₂O₇. The AF order inhomogeneity is found not to be strongly correlated with the charge gap. Interestingly, the AF order in the bi-layered Sr₃Ir₂O₇ shows residual memory behavior with temperature cycling. Overall, our work revealed new phenomena in a range of today’s most intriguing materials and set the stage for using SP-STM in other complex oxides. / Thesis (PhD) — Boston College, 2020. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Physics.

On a longtemps pensé que la communication intercellulaire était essentiellement régie par les signalisations juxta-, endo- et paracrine, les gap junctions et, plus récemment, les exosomes. Cependant, les travaux de plusieurs groupes dont le nôtre ont révélé que les Tunneling Nanotubes (TNT), des protrusions membranaires riches en actine qui relient le cytoplasme de cellules distantes et permettent le transport intercellulaire dynamique de leur contenu biologique, fournissent également l'infrastructure et les machines pour une communication efficace entre cellules. Malgré des progrès significatifs, la caractérisation de ces nouveaux organites a été limitée par le manque d'informations moléculaires et structurelles. Combler ces lacunes à l'aide d'une série d'outils de pointe et d'approches novatrices est devenu l'objectif principal de ma thèse. Plus précisément, j'ai exploré le rôle des complexes régulateurs de l’actine dans la formation des TNT reliant les cellules neuronales. Mes analyses montrent que les voies moléculaires connues pour être impliquées dans la formation d'autres protrusions membranaires régulent différemment la génération des TNT. En utilisant la microscopie par imagerie en direct, la microscopie électronique cryocorrélative et la tomographie, j'ai également étudié la nano-architecture des TNT neuronaux. Mes découvertes ont démontré que les TNT des cellules neuronales sont composés de plusieurs TNT individuels permettant le passage de vésicules et de mitochondries. En raison des difficultés d'identification des TNT in vivo, mes travaux ont également porté sur la mise en œuvre d'une approche « Connectomic » structurelle pour détecter les TNT dans les tissus sans avoir besoin d'un marqueur spécifique de TNT. Mes résultats indiquent que des structures de type TNT relient les cellules granulaires cérébelleuses migratrices des souris nouveau-nées, ce qui suggère que la communication intercellulaire pendant des événements migratoires dans le cerveau pourrait être médiée par des processus mettant en jeu des TNT. La squelettisation des structures identifiées fournit des informations géométriques qui corroborent les observations faites dans des expériences de couplage de colorants. L'ensemble de mes travaux de thèse fait la lumière sur la formation et la structure des TNT neuronaux in vitro et sur de nouvelles approches pour l'identification des TNT in vivo. / Inter-cellular communication has long been thought to be governed by juxta-, endo-, and paracrine signaling, tight junctions, and more recently, exosomes. However, large efforts from our and other groups revealed that Tunneling Nanotubes (TNTs), actin-rich membranous protrusions that connect the cytoplasm of distant cells and allow the dynamic inter-cellular transport of biological cargo, also provide the infrastructure and machinery for effective cell-to-cell communication. Despite significant progress made to unveil TNT-mediated cell communication, the characterization of these novel organelles has been limited by unanswered questions that hail from the lack of both molecular and structural information. Exploring these gaps in the field using a series of state-of-the-art tools and novel approaches became the main focus of my dissertation. Specifically, I explored the specific role of actin-regulator complexes in the formation of TNTs connecting neuronal cells. My analyses show that molecular pathways known to be involved in the formation of other membranous protrusions behave differently in the generation of TNTs. By employing live imaging microscopy, cryo-correlative electron microscopy and tomography approaches, I also studied the nano- architecture of neuronal TNTs. My findings demonstrated that TNTs of neuronal cells are comprised of multiple individual TNTs capable of transporting vesicles and mitochondria. Owing to the difficulties of identifying TNTs in vivo, my work also focused on the implementation of a structural Connectomic approach to detect TNTs in tissue without the need for a TNT-specific marker. My findings indicate that TNT-like structures connect migratory cerebellar granule cells of neonate mice, suggesting that inter-cellular communication during migratory events in the brain could be mediated by TNT-like processes. Skeletonization of the structures identified provide my findings with geometrical information that can be compared with observations made by corroborative dye-coupling experiments. Taken together, my dissertation work sheds light on the formation and structure of neuronal TNTs in vitro, and novel approaches for the identification of TNTs in vivo.

No description available.

Radio frequency (RF) cavities are the foundational infrastructure which facilitates much of the fundamental research conducted in high energy particle physics. These RF cavities utilize their unique shape to produce resonant electromagnetic fields used to accelerate charged particles. Beside their core role in fundamental physics research, RF cavities have found application in other disciplines including material science, chemistry and biology which take advantage of their unique light sources. Industry has been keen on taking advantage of accelerator technology for a multitude of applications. Particle accelerators like the one found at Jefferson Lab’s Continuous Electron Beam Accelerator Facility must produce stable beams of high energy particles which is an incredibly costly endeavor to pursue. With the gargantuan size of these facilities, the cost of high-quality beam production is a matter of great importance. The quest to find highly efficient RF cavities has resulted in the widespread use of superconducting radio frequency (SRF) cavities which are the most efficient resonators that exploit a superconductor’s incredibly low AC surface resistance. While metals like Cu are up to the demanding job of RF cavity particle acceleration, their efficiency at transferring RF power to the particle beam is low when they are compared with SRF Nb cavities. Nb is the standard material for all SRF cavity technology particularly for its reproducibly low surface resistance, comparatively high transition temperature and thermodynamic critical field. Using superconducting Nb is not without its drawbacks. Keeping hundreds of Nb cavities in their superconducting state under extreme RF conditions is quite a daunting task. It requires the normal state not nucleate during operation. This is achieved by producing high-quality cavities with as few defects and impurities as possible while also keeping the cavities at low temperature, usually 2K. Again, due to the sheer scale of the facilities, hundred million-dollar cryogenic plants are required to handle the heat loads during SRF cavity operation. This means even small increases in maximum accelerating gradients or decrease in cavity surface resistance results in a sizably reduced operation cost. Considerable effort has been put forth to increase the efficiency of Nb cavities toward and even beyond the theoretical maximum accelerating gradients and quality factor for a clean superconductor. Recently, a new method to produce high quality factor cavities has emerged that involves nitrogen doping the cavity. The mechanism by which N doping causes the improvement is still not well understood, but the experimental research described in this dissertation shines some light into the mechanisms behind such a drastic improvement. These insights are universal for all superconductors and may prove useful for SRF cavities beyond Nb. With Nb approaching its fundamental limits, new materials are being proposed to increase the performance of future SRF cavities which MgB2 finds itself among. MgB2 is a two-band superconductor that possesses many properties that are very attractive for the next generation of SRF cavities. One of the most important properties is MgB2’s comparatively large critical temperature which in part predicts it will have a lower surface resistance than Nb at higher operating temperatures. Such behavior of MgB2 may unlock the possibility of using cryocoolers instead of costly liquid helium plants for large scale industrial use. This dissertation starts with an introduction to superconductivity, its theory, and application to SRF cavities as well as the open questions that can be addressed in Nb and the next generation of SRF materials. A description of the experimental techniques of scanning tunneling microscopy, X-ray photoelectron spectroscopy, and atomic force microscopy is presented. Our experimental investigation into Nb SRF cavity cutouts starts with a discussion of the material’s limitations for SRF applications with an emphasis on the proximity effect which arises at the surface of this material due to its myriad of naturally forming oxides. The results of our scanning tunneling microscopy measurements for typically prepared Nb and nitrogen doped Nb follows and comparisons are made which show that the surface oxides are fundamentally different between these samples likely resulting in the profound enhancement of the cavity’s quality factor. Experimental investigation into the native oxide of hot spot nitrogen doped Nb shows a degraded oxide and superconducting properties as compared with the cold spot. The dissertation continues with a brief introduction to MgB2, followed by our scanning tunneling and electron tunneling insights into MgB2. The dissertation is concluded with a summary of our investigations and broader impact of our research on the SRF community. / Physics

Two dimensional (2D) materials, including graphene, hexagonal boron nitride and layered transition metal dichalcogenides (TMDs), have been a revolution in condensed matter physics and they are at the forefront of recent scientific research. They are being explored for their unusual electronic, optical and magnetic properties with special interest in their potential uses for sensing, information processing and memory. Molybdenum disulfide (MoS2) has been the flagship semiconducting TMD over the past ten years due to its unique electronic, optical and mechanical properties. In this thesis, we grow mono- to few layer MoS2 films using ambient pressure chemical vapor depositions (AP-CVD) to obtain high quality samples. We employ low temperature scanning tunneling microscopy and spectroscopy (LT-STM/STS) to study the effect of layer number on the electronic density of states (DOS) of MoS¬2. We find a reduction of the magnitude of the quasiparticle band gap from one to two monolayers (MLs) thick. This reduction is found to be due mainly to a shift of the valence band maxima (VBM) where the conduction band minimum (CBM) does not change dramatically. Density functional theory (DFT) modeling of this system shows that the overlap of the interfacial S-pz orbitals is responsible for shifting the valence band edge at the Γ-point toward the Fermi level (EF), reducing the magnitude of the band gap. Additionally, we show that the crystallographic orientation of monolayer MoS2 with respect to the HOPG substrate can also affect the electronic DOS. This is demonstrated with five different monolayer regions having each with a unique relative crystallographic orientation to the underlying substrate. We find that the quasiparticle band gap is closely related to the moiré pattern periodicity, specifically the larger the moiré periodicity the larger the band gap. Using DFT, we find that artificially increasing the interaction between the film and the substrate means that the magnitude of the band gap reduces. This indicates that the moiré pattern period acts like a barometer for interlayer coupling. We investigate the effect of defects, both point and extended defects, on the electronic properties of mono- to few layer MoS¬2 films. Atomic point defects such including Mo interstitials, S vacancies and O substitutions are identified by STM topography. Two adjacent defects were investigated spectroscopically and found to greatly reduce the quasiparticle band gap and arguments were made to suggest that they are Mo-Sx complex vacancies. Similarly, grain boundaries were found to reduce the band gap to approximately ¼ of the gap found on the pristine film. We use Kelvin probe force microscopy (KPFM) to investigate the affect of annealing the films in UHV. The work function measurements show metastable states are created after the annealing that relax over time to equilibrium values of the work function. Scanning transmission electron microscopy (STEM) is used to show that S vacancies can recombine over time offering a feasible mechanism for the work function changes observed in KPFM. Lastly, we report how strain affects the quasiparticle band gap of monolayer MoS2 by bending the substrate using a custom built STM sample holder. We find that the local, atomic-scale strain can be determined by a careful calibration procedure and a modified, real-space Lawler Fujita algorithm. We find that the band gap of MoS2 reduces with strain at a rate of approximately 400 meV/% up to a maximum strain of 3.1%, after which the film can slip with respect to the substrate. We find evidence of this slipping as nanoscale ripples and wrinkling whose local strain fields alter the local electronic DOS. / Physics

The term “electroluminescence” refers to light emission resulting from the application of an electrical bias. Electron tunneling across a biased, nanoscale junction can serve as the excitation source for photon emission. This effect is also mediated by the plasmonic environment of the junction, where a strong local field can enhance light emission by orders of magnitude. This dissertation presents measurements of electroluminescence from nanoscale gaps and single-molecule junctions. These measurements are made possible by a custom light emission detection system coupled to a scanning tunneling microscope break junction (STM-BJ) instrument. Conductance and light emission data are obtained simultaneously for thousands of junctions. Chapter 1 discusses molecular optoelectronics, a field at the intersection of plasmonic phenomena and molecular electronics, and introduces the STM-BJ technique for measuring molecular junctions. Chapter 2 describes the light emission detection setup that is operated in tandem with the STM-BJ instrument. Chapter 3 presents a study of Au tunnel junctions. This lays the groundwork for the plasmonics at play in these electroluminescent systems, detangling how gap size, electrical bias, and emission wavelength affect plasmonic enhancement. In Chapters 4 and 5, Au-molecule-Au junctions are investigated in some of the first experimental studies of single-molecule electroluminescence at ambient conditions. Chapter 4 uses light emission data from molecular junctions to estimate finite-frequency shot noise and uncover critical information about transmission characteristics. Chapter 5 presents one of the first examples of single-molecule strong light-matter coupling in an electroluminescent system, substantiated by spectroscopy data. This dissertation greatly expands on existing knowledge of plasmonic phenomena, particularly in relation to electroluminescent devices. Furthermore, it lays a strong foundation for single-molecule spectroscopy studies using the STM-BJ technique.