The objective of this research is to present a set of powerful simulation, design, and characterization tools suitable for studying novel nanophotonic devices. The simulation tools include a three-dimensional finite-difference time-domain code adapted for parallel computing that allows for a wide range of simulation conditions and material properties to be studied, as well as a semi-analytical Green's function-based complex mode technique for studying loss in photonic crystal waveguides. The design tools consist of multifunctional photonic crystal-based template that has been simulated with nonlinear effects and measured experimentally, and planar slab waveguide structure that provides highly efficient second harmonic generation is a chip-scale device suitable for photonic integrated circuit applications. The characterization tool is composed of a phase-sensitive measurement system using a lock-in amplifier and high-precision optical stages, suitable for probing the optical characteristics of nanoscale devices. The high signal-to-noise ratio and phase shift data provided by the lock-in amplifier allow for accurate transmission measurements as well as a phase spectrum that contains information about the propagation behavior of the device beyond what is provided by the amplitude spectrum alone.

The exceptional self-assembly properties of DNA as well as its ability to interact with different kinds of chemical compounds and biological structures make this biomolecule to an interesting object for the fabrication of artificial nanostructures. In this work several methods for a DNA-based self-assembly of electronic nanocircuitry are explored. For this, four basic steps, which turned out to be essential within a circuit assembly process, are addressed: (i) The formation of multi-branched DNA junctions by a simple building-block procedure. (ii) The site-specific attachment of nanoobjects (gold colloids) at the center of DNA junctions. (iii) The integration of DNA into microstructured gold electrode arrays, in particular the stretching of single DNA molecules between two electrodes. For this a simple, but reliable methods for the functionalization of gold electrodes by using aminoethanethiol was developed, which enables end-specific attachment of the DNA but does not require DNA modification. (iv) The metallization of DNA. A synthesis procedure was developed, which results in the formation of continuous chains of 5nm platinum clusters along the DNA. The metal deposition process turned out to take place exclusively at the DNA while background metallization is completely suppressed.

Spectroscopic second-harmonic generation (SHG) and reflectance-anisotropy spectroscopy (RAS) are used to probe molecular adsorption on clean reconstructed single-domain stepped Si(001) in ultra-high vacuum (UHV). We implement a simplified bond hyperpolarizability model (SBHM) as a common microscopic analysis for SHG and RAS. Three different scenarios are studied: (i) The dissociative adsorption of molecular hydrogen on dangling bonds of D[subscript B] step-edges. (ii) Structural changes to rebonded r-D[subscript B] steps induced by exposure to atomic hydrogen. (iii) The adsorption of cyclopentene on Si(001)(2x1) terrace dimers in a [2+2] cycloaddition pathway. Using the SBHM we develop a new optical fingerprinting method to isolate, identify and monitor individual types of bonds (e.g. dimers, rebonds, dangling bonds, backbonds) and their chemical activity on a single-domain stepped Si(001) surface using nonresonant, but rotationally-anisotropic, second-harmonic generation (RA-SHG). The methods presented here will be applicable to many material systems and allow to track, in-situ and in real-time, the chemical action of adsorbates on surfaces. / text

This dissertation research is focused on first principles studies of graphene and single organic molecules for nanoelectronics applications. These nanosized objects attracted considerable interest from the scientific community due to their promise to serve as building blocks of nanoelectronic devices with low power consumption, high stability, rich functionality, scalability, and unique potentials for device integration. Both graphene electronics and molecular electronics pursue the same goal by using two different approaches: top-down approach for graphene devices scaling to smaller and smaller dimensions, and bottom-up approach for single molecule devices. One of the goals of this PhD research is to apply first-principles density functional theory (DFT) to study graphene/metal and molecule/metal contacts at atomic level. In addition, the DFT-based approach allowed us to predict the electronic characteristics of single molecular devices. The ideal and defective graphene/metal interfaces in weak and strong coupling regimes were systematically studied to aid experimentalists in understanding graphene growth. In addition, a theory of resonant charge transport in molecular tunnel junctions has been developed. The first part of this dissertation is devoted to the study of atomic, electronic, electric, and thermal properties of molecular tunnel junctions. After describing the model and justifying the approximations that have been made, the theory of resonant charge transport is introduced to explain the nature of current rectification within a chemically asymmetric molecule. The interaction of the tunneling charges (electrons and holes) with the electron density of the metal electrodes, which in classical physics is described using the notion of an image potential, are taken into account at the quantum-mechanical level within the tight binding formalism. The amount of energy released onto a molecule by tunneling electrons and holes in the form of thermal vibration excitations is related to the reorganization energy of the molecule, which is also responsible for an effective broadening of molecular levels. It was also predicted that due to the asymmetry of electron and hole resonant energy levels with respect to the Fermi energy of the electrodes, the Joule heating released from the metallic electrodes is also non-symmetric and can be used for the experimental determination of the type of charge carriers contributing to the molecular conductance. In the second part of the dissertation research ideal and defective graphene/metal interfaces are studied in weak and strong interface coupling regimes. The theoretical predictions suggest that the interface coupling may be controlled by depositing an extra metallic layer on top of the graphene. DFT calculations were performed to evaluate the stability of a surface nickel carbide, and to study graphene/carbide phase coexistence at initial stages of graphene growth on Ni(111) substrate at low growth temperatures. Point defects in graphene were also investigated by DFT, which showed that the defect formation energy is reduced due to interfacial interactions with the substrate, the effect being more pronounced in chemisorbed graphene on Ni(111) substrate than in physisorbed graphene on Cu(111) substrate. Our findings are correlated with recent experiments that demonstrated the local etching of transfered graphene by metal substrate imperfections. Both graphene and molecular electronics components of the PhD dissertation research were conducted in close collaboration with several experimental groups at the University of South Florida, Brookhaven National Laboratory, University of Chicago, and Arizona State University.

Der Elektronentransport durch Nanostrukturen bietet eine Perspektive auf interessante Anwendungen und neue Einsichten in die Nichtgleichgewichtsdynamik von Elektronen in komplexen Umgebungen. Quantendotsysteme erlauben im Speziellen ein hohes Maß an Kontrolle ihrer Eigenschaften und ermöglichen damit detaillierte Untersuchungen. Das wachsende Interesse an zeitaufgelöstem Elektronentransport in diesen Systemen erklärt sich vor allem durch die rasanten Fortschritte bei der experimentellen Realisierung von pulsinduziertem Transport. Zur Beschreibung und Interpretation dieser Experimente bedarf es der Entwicklung neuer theoretischer Zugänge und Berechnungsverfahren. In dieser Arbeit werden zwei Propagationsmethoden zur numerischen Beschreibung von zeitaufgelöstem Elektronentransport entwickelt. Hierbei wird einerseits von einer Einteilchenbeschreibung mit Nichtgleichgewichts-Green-Funktionen (NEGF) und andererseits von einer Vielteilchenbeschreibung, basierend auf verallgemeinerten Quantenmastergleichungen für die reduzierte Vielteilchendichtematrix, ausgegangen. Das Konzept ist in beiden Fällen ähnlich: Im ersten Schritt der Herleitung werden Hilfsgrößen eingeführt und gleichberechtigt zum reduzierten Zustand des Systems behandelt. Eine Hilfsmodenentwicklung der Fermi-Funktion ermöglicht im zweiten Schritt die numerische Berechnung mit den hergeleiteten Bewegungsgleichungen. Mit Hilfe einer Partialbruchzerlegung wird eine Entwicklung der Fermi-Funktion abgeleitet, die sich durch eine wesentlich verbesserte Konvergenz gegenüber bisher bekannten Entwicklungen auszeichnet. Diese Zerlegung erweist sich für die Propagation als effizienter Zugang und kann darüber hinaus bei Berechnungen zur Elektronenstruktur angewendet werden. Obwohl der NEGF-Formalismus eines der Standardverfahren für die Behandlung von Transportdynamik in Nanostrukturen darstellt, ist die Auswahl an numerischen Implementierungen verschwindend gering. Die in dieser Arbeit entwickelte Propagationsmethode stellt eine neue Herangehensweise dar, die im Vergleich zu den bisherigen Zugängen ein günstigeres Skalierungsverhalten aufweist. Anhand von zwei Beispielen wird demonstriert, dass die Methode sowohl auf stochastisch getriebene Systeme als auch auf Situationen mit realistischen Spannungspulsen anwendbar ist. Eine Erweiterung auf wechselwirkende Elektronen wird ausgehend von der Methode der Bewegungsgleichungen abgeleitet. Im Rahmen der Vielteilchenbeschreibung durch die verallgemeinerten Quantenmastergleichungen wird insbesondere der Einfluss von Termen höherer Ordnung untersucht. Hierzu wird, neben der üblichen Quantenmastergleichung zweiter Ordnung, explizit die vierte Ordnung berechnet. Ein Vergleich mit dem NEGF-Formalismus zeigt die Notwendigkeit höhere Ordnungen, zumindest partiell, zu berücksichtigen, da erst hierdurch die Verbreiterung der Energieniveaus aufgrund der Tunnelkopplung an die Reservoirs konsistent beschrieben wird. Dieser Befund wird am Beispiel des stationären und transienten Elektronentransports durch einen Doppelquantendot untermauert. Auf der Basis von numerischen Berechnungen und einem analytisch lösbaren Modell werden die Resultate eines aktuellen Pump-Probe-Experiments zur kohärenten Kontrolle von Ladungs-Qubits in Doppelquantendots interpretiert. Die Anwendungsmöglichkeiten der entwickelten Propagationsmethoden gehen weit über die in der Arbeit betrachteten Beispiele hinaus. Sie erlauben die Beschreibung von neuartigen Transportkonzepten und ermöglichen einen erweiterten Einblick in die Nichtgleichgewichtsdynamik von Elektronen in Nanostrukturen.

Graphene, a honeycomb lattice of sp2-bonded carbon atoms, has received considerable attention in the scientific community due to its unique electronic properties. Distinct symmetries of the graphene wave functions lead to unusual quantum properties, such as a unique half-integer quantum Hall effect. As an added consequence of these symmetries, back-scattering in graphene is strongly prohibited leading to long coherence lengths of carriers. These charge carriers at low energy exhibit linear energy-momentum dispersion, much like neutrinos. Thus, carriers in graphene can be described as massless Dirac fermions. Graphene grown epitaxially on semiconducting substrates offers the possibility of large-scale production and deterministic patterning of graphene for nanoelectronics. In this work, epitaxial graphene is created on SiC(0001) by annealing in vacuum. Sequential scanning tunneling microscopy (STM) and spectroscopy (STS) are performed in ultrahigh vacuum at a temperature of 4.2 K and 300 K. These atomic-scale studies address the growth, interfacial properties, stacking order, and quasiparticle coherence in epitaxial graphene. STM topographic images show the atomic structure of successive graphene layers on the SiC substrate, as well as the character of defects and adatoms within and below the graphene plane. STS differential conductance (dI/dV) maps provide spatially and energy resolved snapshots of the local density of states. Such maps clearly show that scattering from atomic defects in graphene gives rise to energy-dependent standing wave patterns. We derive the carrier energy dispersion of epitaxial graphene from these data sets by quantifying the dominant wave vectors of the standing waves for each tunneling bias.

Le graphène possède un gaz bidimensionnel de porteurs de charge stable et exposé à l'environnement sans aucune protection. Par conséquent, ses performances électriques sont extrêmement sensibles aux conditions environnementales, notamment aux impuretés chargées et aux corrugations imposées par le substrat sous-jacent. Ces éléments ont une contribution majeure dans la dégradation des propriétés de transport électronique du matériau.L'objectif de cette thèse est d'explorer par diverses techniques des méthodes pour atténuer ces effets par optimisation de son environnement direct.La première méthode consiste à reporter le graphènesur une couche neutre d'un cristal de nitrure de bore hexagonal (BN). Diverses techniques de fabrication d'empilement de Graphène sur BN sont présentées, notamment la croissance directe de graphène sur un cristal de BN exfolié sur un substrat catalytique qui aboutit à la formation d'empilements de structure bien contrôlée. Les échantillons sont mesurés à très basse température. Les effets de localisation faible mesurés par magnéto-transport montrent une amélioration nette des performances notamment de la longueur de cohérence et de la mobilité électronique par rapport à un échantillon de référence constitué du même ruban de graphène déposé sur substrat conventionnel de silicium oxydé.La deuxième technique consiste à isoler le graphène de son support par surgravure de la silice et suspension du graphène sous la forme d'une membrane autosupportée et tenue par ses extrémités. Après avoir introduit des techniques de fabrication spécifiques, les mesures de transport et le couplage à des modes de vibration mécanique sont étudiés température variable. Ces données permettent notamment une mesure du coefficient d'expansion thermique du graphène. / Charge carriers in graphene form stable two-dimensional gases which are fully exposed to the environment. As a consequence, the electrical performance of graphene is strongly affected by surface charged impurities as well as topographic perturbations inherited from the underlying substrate.This thesis addresses several methods to circumvent that issue.The first method consists in embedding graphene in an optimized environment by depositing graphene onto some neutral and crystalline material. Novel 2D insulating materials such as hexagonal boron nitride buffer layer (BN) appears as ideal substrates to get rid of detrimental effect of interfacial charges and corrugation. Several fabrication schemes of Graphene/BN stacks are shown including some direct in-situ growth of graphene on BN crystal using an innovative proximity-driven chemical vapour growth based on BN exfoliation on copper. In order to explore the effects of the improved substrate on the transport properties of graphene, we have performed low temperature magneto-transport studies on these stacks. We present a direct comparison of weak localization signals with those acquired on a graphene/silica reference device. A clear increase of the coherence length is shown on Graphene/BN stacks together with improved electronic mobility and charge neutrality.Removing the substrate and suspending graphene is another approach for optimization of the graphene environment which forms the second topic covered in this thesis. After introducing an improved recipe for preserving the quality of graphene throughout an elaborate fabrication process, we probe the room- and low-temperature performance of the nano-electro-mechanical devices based on doubly clamped suspended graphene ribbons. The obtained data are used for characterizing the thermal expansion of CVD graphene.

Le graphène héberge un gaz d'électrons bi-dimensionnel, sujet à un potentiel électrostatique désordonné dû aux impuretés de charge dans le substrat. Ce potentiel désordonné induit des inhomogénéités de la densité de porteurs de charge dans le graphène. Par ailleurs, l'écrantage dans le graphène mono-feuillet de ce potentiel dépend lui-même de la densité de porteurs de charge. L'effet du désordre de charge peut donc être modulé avec un potentiel de grille global, ce qui se manifeste en particulier dans la transconductance de dispositifs à base de graphène. Nous combinons des mesures par Microscopie/Spectroscopie à effet tunnel avec des mesures de transport in situ sur des dispositifs à base de mono-feuillets de graphène sur SiO2, à basse température. Les cartes de la densité locale d'états du graphène, à diverses tensions de grille, mettent en évidence l'augmentation progressive des dimensions latérales ainsi que de l'amplitude des inhomogénéités au voisinage du point de Dirac. Alors que la dépendance en grille de la taille des inhomogénéités est en bon accord avec les prédictions, leur amplitude est plus forte qu'attendue au point de Dirac. Nous expliquons ce désaccord en prenant en compte l'effet de grille local produit par la pointe elle-même, qui a pour effet d'amplifier expérimentalement toute variation de la densité de porteurs de charge lorsque celle-ci elle faible. Cette expérience est ainsi la première mesure qui relie quantitativement les propriétés de désordre de charge à l'échelle microscopique aux propriétés de transport macroscopiques d'un dispositif à base de graphène. / Graphene presents a two-dimensional system whose charge carriers are subjected to a disordered potential created by random charge impurities trapped in the substrate. This impurity potential induces an inhomogeneous carrier concentration. On the other hand, the ability of single-layered graphene to screen this potential strongly depends on the charge carrier density. Thus the effect of the resulting charge disorder can be tuned with the backgate which manifests also in the transport properties of the device. By combining Scanning tunneling microscopy and spectroscopy with in-situ transport at dilution temperature, we probe a system of single-layered graphene on SiO2. Local density of states maps on graphene, acquired at various carrier concentrations show gradual increase of spatial extent and amplitude of inhomogeneities as the Dirac point is approached. While the variations of the spatial extent of the fluctuations with back-gate show very good agreement with predictions, the observed amplitude of inhomogeneities show a larger than expected increase at low densities. We explain this as a result of the local gating effect exerted by the tip on graphene which amplifies any change in the intrinsic doping at low carrier concentrations. This is the first experiment bridging the gap between microscopic disorder and macroscopic transport properties of a graphene device.

Our vision is as yet unsurpassed by machines because of the sophisticated representations of objects in our brains. This representation is vastly different from a pixel-based representation used in machine storages. It is this sophisticated representation that enables us to perceive two faces as very different, i.e, they are far apart in the “perceptual space”, even though they are close to each other in their pixel-based representations. Neuroscientists have proposed distances between responses of neurons to the images (as measured in macaque monkeys) as a quantification of the “perceptual distance” between the images. Let us call these neuronal dissimilarity indices of perceptual distances. They have also proposed behavioural experiments to quantify these perceptual distances. Human subjects are asked to identify, as quickly as possible, an oddball image embedded among multiple distractor images. The reciprocal of the search times for identifying the oddball is taken as a measure of perceptual distance between the oddball and the distractor. Let us call such estimates as behavioural dissimilarity indices. In this thesis, we describe a decision-theoretic model for visual search that suggests a connection between these two notions of perceptual distances. In the first part of the thesis, we model visual search as an active sequential hypothesis testing problem. Our analysis suggests an appropriate neuronal dissimilarity index which correlates strongly with the reciprocal of search times. We also consider a number of alternative possibilities such as relative entropy (Kullback-Leibler divergence), the Chernoff entropy and the L1-distance associated with the neuronal firing rate profiles. We then come up with a means to rank the various neuronal dissimilarity indices based on how well they explain the behavioural observations. Our proposed dissimilarity index does better than the other three, followed by relative entropy, then Chernoff entropy and then L1 distance. In the second part of the thesis, we consider a scenario where the subject has to find an oddball image, but without any prior knowledge of the oddball and distractor images. Equivalently, in the neuronal space, the task for the decision maker is to find the image that elicits firing rates different from the others. Here, the decision maker has to “learn” the underlying statistics and then make a decision on the oddball. We model this scenario as one of detecting an odd Poisson point process having a rate different from the common rate of the others. The revised model suggests a new neuronal dissimilarity index. The new dissimilarity index is also strongly correlated with the behavioural data. However, the new dissimilarity index performs worse than the dissimilarity index proposed in the first part on existing behavioural data. The degradation in performance may be attributed to the experimental setup used for the current behavioural tasks, where search tasks associated with a given image pair were sequenced one after another, thereby possibly cueing the subject about the upcoming image pair, and thus violating the assumption of this part on the lack of prior knowledge of the image pairs to the decision maker. In conclusion, the thesis provides a framework for connecting the perceptual distances in the neuronal and the behavioural spaces. Our framework can possibly be used to analyze the connection between the neuronal space and the behavioural space for various other behavioural tasks.

Microfluidics miniaturizes many benchtop processes and provides advantages of low cost, reduced reagent usage, process integration, and faster analyses. Microfluidic devices have been fabricated from a wide variety of materials and methods for many applications. This dissertation describes four such examples, each employing different features and fabrication methods or materials in order to achieve their respective goals. In the first example of microfluidic applications in this dissertation, thermoplastics are hot embossed to form t-shaped channels for microchip electrophoresis. These devices are used to separate six preterm birth (PTB) biomarkers and establish a limit of detection for each. The next chapter describes 3D printed devices with reversed-phase monoliths for solid-phase extraction and on-chip fluorescent labeling of PTB biomarkers. I demonstrate the optimization of the monolith and selective retention of nine PTB biomarkers, the first microchip study to perform an analysis on this entire panel. The third project describes the iterative design and fabrication of glass/polydimethylsiloxane (PDMS) devices with gold and nickel electrodes for the self-assembly of DNA nanotubes for site-selective placement of nanowires. Simple flow channels and “patch electrode” devices were successfully used, and DNA seeding was achieved on gold electrodes. Finally, a 3D printed device for cancer drug screening was developed as a replacement for one previously fabricated in PDMS. Devices of increasing complexity were fabricated, and those tested found to give good control over fluid flow for multiple inlets and valves. Although the applications and methods of these projects are varied, the work in this dissertation demonstrates the potential of microfluidics in several fields, particularly for diagnostics, therapeutics, and nanoelectronics. Furthermore, it demonstrates the importance of applying appropriate tools to each problem to gain specific advantages. Each of the described devices has the potential for increased complexity and integration, which further emphasizes the advantages of miniaturized analyses and the potential for microfluidics for analytical testing in years to come.