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As the scaling of CMOS approaches fundamental limits, revolutionary technology beyond the end of CMOS roadmap is essential to continue the progress and miniaturization of integrated circuits. Recent research efforts in 3-D circuit integration explore pathways of continuing the scaling by co-designing for device, circuit, connectivity, heat and manufacturing challenges in a 3-D fabric-centric manner. SkyBridge fabric is one such approach that addresses fine-grained integration in 3-D, achieves orders of magnitude benefits over projected scaled 2-D CMOS, and provides a pathway for continuing scaling beyond 2-D CMOS. However, SkyBridge fabric utilizes only single type transistors in order to reduce manufacture complexity, which limits its circuit implementation to dynamic logic. This design choice introduces multiple challenges for SkyBridge such as high switching power consumption, susceptibility to noise, and increased complexity for clocking. In this thesis we propose a new 3-D fabric, similar in mindset to SkyBridge, but with static logic circuit implementation in order to mitigate the afore-mentioned challenges. We present an integrated framework to realize static circuits with vertical nanowires, and co-design it across all layers spanning fundamental fabric structures to large circuits. The new fabric, named as SkyBridge-CMOS, introduces new technology, structures and circuit designs to meet the additional requirements for implementing static circuits. One of the critical challenges addressed here is integrating both n-type and p-type nanowires. Molecular bonding process allows precise control between different doping regions, and novel fabric components are proposed to achieve 3-D routing between various doping regions. Core fabric components are designed, optimized and modeled with their physical level information taken into account. Based on these basic structures we design and evaluate various logic gates, arithmetic circuits and SRAM in terms of power, area footprint and delay. A comprehensive evaluation methodology spanning material/device level to circuit level is followed. Benchmarking against 16nm 2-D CMOS shows significant improvement of up to 50X in area footprint and 9.3X in total power efficiency for low power applications, and 3X in throughput for high performance applications. Also, better noise resilience and better power efficiency can be guaranteed when compared with original SkyBridge fabrics.

Electrochemical synthesis of straight, separable, cylindrical nanowires for use as cantilevered mechanical resonators is the main focus of this dissertation. These types of nanowires are significant for many applications, but particularly so for chip-based sensor arrays made for ultrasensitive mass detection. Directed-assembly of nanowire-based devices has enabled the development of large-area fabrication of sensor devices with new functions such as cancer detection at early stage. Chemically stable noble metals gold and rhodium are interesting materials for making nanowire resonators. Gold makes a well-known, stable and strong bond with the thiol group, which enables a range of surface functionalization chemistries. Rhodium nanowires have desirable mechanical properties for resonant mass sensing as they can retain high quality factor (Q-factor) from high vacuum to near atmospheric pressures. As a versatile and inexpensive tool, electrodeposition provides the most suitable synthesis path for gold and rhodium resonator-grade nanowires in nanoporous templates. In this work, the structural characteristics of nanoporous membranes anodized aluminium oxide and track-etched polycarbonate was explored for use as electrodeposition template. New chemistries for making gold and rhodium nanowires are introduced. Although gold cyanide-based solutions work well for the electrochemical synthesis of separable nanowires, the toxicity of cyanide solutions makes non-cyanide alternatives desirable. However, electrochemical synthesis of gold nanowires in templates from non-cyanide solutions suffers from serious drawbacks. These include growth-arresting pellet formation, poor length control and defects such as inclusions. In this dissertation, the first electrochemical synthesis of straight, cylindrical, separable gold nanowires from a sulfite-based solution is presented. This work demonstrates a scheme that suppresses electroless particle growth in the weakly-complexed gold in solution by proper use of additives. The electrochemical nucleation and growth of rhodium nanowires from a sulphate-based solution is also discussed. The effect of pH on the length uniformity as well as the effect of EDTA and polyethylenimine as additives on the development of the wire nanostructure was studied. This study has shown that the control over hydrogen co-reduction on the electrode surface and its bubble transport rate allowed for tailoring the nanostructure of the grown nanowires. The control over electrochemical nucleation and growth of noble metal films for nanowire clamping has also been investigated in this work for making reliable defect-free clamps for nanoresonator measurements. Silver was introduced as a reliable replacement for gold for nanowire clamping. Resonance measurements of rhodium nanowires clamped with silver, confirmed a reliable and repeatable clamp with very small scatter in the plot of resonance frequency variation with appropriate geometric terms. In addition, we found that the elastic modulus of a set of rhodium nanowires synthesized and measured in this work, was 14% larger than in previous studies. / Graduate / 0794 / 0548 / mascotella@gmail.com

Silicon nanowires (SiNWs) and the copper chalcogenides, namely copper sulfide (Cu2S) and selenide Cu2Se, have diverse applications in renewable energy technology. For example, SiNWs which have direct band gaps unlike bulk Si, have the potential to radically reduce the cost of Si based photovoltaic cells. However, they degrade quickly under ambient conditions. Various surface passivations have therefore been investigated for enhancing their stability but it is not yet well understood how they affect the electronic structure of SiNWs at a fundamental level. Here, we will explore, from first-principles simulation, how fluorine, methyl and hydrogen surface passivations alter the electronic structures of [111] and [110] SiNWs via strain and quantum confinement. We also show how electronic charge states in [111] and [110] SiNWs can be effectively modelled by simple quantum wells. In addition, we address the issue of why [111] SiNWs are less influenced by their surface passivation than [110] SiNWs. Like SiNWs, Cu2S and Cu2Se also make excellent photovoltaic cells. However, they are most well known for their exceptional thermoelectric performance. This is by virtue of their even more unique solid-liquid hybrid nature which combines the low thermal conductivity and good electrical characteristics required for a high thermoelectric efficiency. We use first-principles molecular dynamics simulations to show that Cu diffusion rates in Cu2S and Cu2Se can be as high as 10-5cm2s-1. We also relate their phonon power spectra to their low thermal conductivities. Furthermore, we evaluate the thermoelectric properties of Cu2S and Cu2Se using a combination of Boltzmann transport theory and first-principles electronic structure calculations. Our results show that both Cu2S and Cu2Se are capable of maintaining high Seebeck coefficients in excess of 200μVK-1 for hole concentrations as high as 3x1020cm-3.

This thesis covers a wide variety of projects within the domain of computational structural biology. Structural biology is concerned with the molecular structure of proteins and nucleic acids, and the relationship between structure and biological function. We used molecular modeling and simulation, a purely computational approach, to study DNA-linked molecular nanowires. We developed a computational tool that allows potential designs to be screened for viability, and then we used molecular dynamics (MD) simulations to test their stability. As an example of using molecular modeling to create experimentally testable hypotheses, we were able to suggest a new design based on pyrrylene vinylene monomers. In another project, we combined experiments and molecular modeling to gain insight into factors that influence the kinetic binding dynamics of fibrin "knob" peptides and complementary "holes." Molecular dynamics simulations provided helpful information about potential peptide structural conformations and intrachain interactions that may influence binding properties. The remaining projects discussed in this thesis all deal with RNA structure. The underlying approach for these studies is a recently developed chemical probing technology called 2'-hydroxyl acylation analyzed by primer extension (SHAPE). One study focuses on ribosomal RNA, specifically the 23S rRNA from T. thermophilus. We used SHAPE experiments to show that Domain III of the T. thermophilus 23S rRNA is an independently folding domain. This first required the development of our own data processing program for generating quantitative and interpretable data from our SHAPE experiments, due to limitations of existing programs and modifications to the experimental protocol. In another study, we used SHAPE chemistry to study the in vitro transcript of the RNA genome of satellite tobacco mosaic virus (STMV). This involved incorporating the SHAPE data into a secondary structure prediction program. The SHAPE-directed secondary structure of the STMV RNA was highly extended and considerably different from that proposed for the RNA in the intact virion. Finally, analyzing SHAPE data requires navigating a complex data processing pipeline. We review some of the various ways of running a SHAPE experiment, and how this affects the approach to data analysis.

Motivées par des données expérimentales sur la magnétisation de réseau de nanofils de plomb, les résolutions numériques des équations stationnaires de Ginzburg-Landau (GL) se sont focalisées sur les géométries à symétrie axiale. L'effet Meissner, les états représentant un vortex d'Abrikosov ou encore des Vortex Géants (``GiantVortex') centrés à l'origine du cylindre ont alors pu être identifiés sous l’hypothèse d’invariance sous rotation selon l’axe de symétrie du cylindre étudié (modèle à une dimension, 1D). En identifiant le type de transition par le caractère continu ou non du paramètre d'ordre autour du changement de phase, une frontière à l'échelle mésoscopique a également pu être identifiée au travers du modèle 1D. Plus spécifiquement, la limite entre les deux types de transitions décrite par le paramètre phénoménologique κ = λ /ξ ( =1/√2 à l’échelle macroscopique) devient une fonction non constante dépendant à la fois du rayon normalisé, u=R/λ, et de la vorticité L: κ =f(u,L). Les deux longueurs caractéristiques λ et ξ représentent respectivement les longueurs de pénétration et de cohérence d’un échantillon supraconducteur. Une comparaison avec les résultats obtenus par Zharkov permet de valider notre démarche numérique employée pour la résolution numérique des équations de GL à une dimension. En employant un modèle à deux dimensions (2D), la symétrie sous rotation des solutions a également été relâchée. Basée sur le principe de moindre action, la résolution propose alors un schéma numérique indépendant du type d'équations du mouvement à solutionner. Les configurations du type MultiVortex ont alors pu être identifiées, et comparées aux solutions du groupe du Professeur F. Peeters. Ces différents accords ont confirmé la démarche développée. Une modélisation de la magnétisation expérimentale d'un réseau de nanofils a également été développée. De par la taille réduite des nanofils, l'interaction magnétique entre ceux-ci a pu être négligée. La magnétisation totale du réseau est alors construite par une sommation incluant la contribution individuelle en magnétisation de chaque fil, pondérée par un poids reflétant une distribution gaussienne pour les rayons des fils constituant le réseau. La magnétisation individuelle est évidemment obtenue par résolution des équations du mouvement de GL précédemment étudiées avec les modèles 1D et 2D. En ajustant les paramètres libres associés à ce modèle décrivant la magnétisation totale du réseau, les données expérimentales ont pu être reproduites endéans 10% de marge d'erreur, l'intervalle d'incertitude caractéristique de la théorie effective de Ginzburg-Landau. Ces variables attachées au modèle de la magnétisation totale, reprennent la valeur moyenne m et l'écart-type s de la distribution gaussienne, ainsi que les longueurs caractéristiques λ(T) et ξ(T) présentes dans la théorie de GL. Un test totalement indépendant de l'analyse des magnétisations a permis de valider les valeurs déterminées pour la distribution des rayons. Les grandeurs ajustées pour les longueurs λ(T) et ξ(T) ont fait l'objet d'une analyse supplémentaire en termes de leur dépendance en température et du libre parcours moyen des électrons. Malgré l'accord entre les données expérimentales et la magnétisation théorique, il est important de mentionner qu'un paramètre libre supplémentaire, associé à l'apparition de configurations décrivant un vortex magnétique, a dû être introduit. Il modifie empiriquement la métastabilité trop longue en mode champ externe décroissant de l'état décrivant un vortex d'Abrikosov. La correction expulse donc le vortex avant sa prédiction théorique liée à la disparition de la barrière de Bean-Linvingston. Une étude plus approfondie de cette barrière de potentiel fut donc également réalisée. Cependant, elle n'est pas concluante en regard des données expérimentales analysées. Il n'en demeure pas moins que la transition apparaît dans un domaine en champ magnétique cohérent vis-à-vis de la description en énergie libre des états de vorticités voisines d'une unité de quantum de flux magnétique. La correspondance entre les longueurs caractéristiques du modèle phénoménologique de GL et les longueurs issues des théories microscopiques de Pippard et BCS a également abordée. Cette étude permet entre autre de comparer les différentes dépendances possibles en température avec les longueurs obtenues de l'analyse de magnétisation des nanofils en plomb. Au delà de l'accord avec le modèle des deux-fluides de Gorter et Casimir, une extrapolation bien en deçà de la température critique Tc est proposée pour les paramètres phénoménologiques λ(T) et ξ(T) de Ginzburg-Landau. Même si la correspondance entre les magnétisations expérimentales et théoriques semblait déjà l'indiquer, il est possible d'appliquer les équations de Ginzburg-Landau pour décrire le comportement magnétique du plomb bien en deçà de sa température critique. De plus, les paramètres associés possèdent une dépendance tout à fait conforme à une autre théorie empirique, le modèle des deux-fluides. Basée sur le modèle de Pippard, une détermination de la valeur du libre parcours moyen des normaux a également été isolée. Elle justifie alors une distinction entre les deux échantillons analysés en terme de leur degré d'impureté. Les résultats électrons obtenus étant en accord avec les procédures de fabrication des nanofils de plomb, cette nouvelle constatation, positive avec l'expérience, confirme une fois de plus la cohérence du modèle développé pour la magnétisation totale, et justifie l'emploi des équations de GL à toutes les températures en dessous de Tc. / Mesoscopic superconductors are described within the framework of the nonlinear Ginzburg-Landau theory. The two coupled nonlinear equations are solved numerically and we investigate the properties, in particular the order of the transition and the vortex configurations, of cylinders submitted to an external magnetic field. Meissner state, Abrikosov vortices, GiantVortex and MultiVortex solutions are described. The Bean-Livingston barrier in mesoscopic cylinders is also numerically studied. This theoretical work was applied to understand experimental magnetizations of lead nanowires in an array well below the superconducting transition temperature Tc. By freely adjusting the GL phenomenological lengths λ (T) and ξ (T), the experimental magnetization curves are reproduced to within a 10% error margin. The Meissner and the Abrikosov state were also experimentally observed in this apparently type-I superconductor. This fact is a consequence of the non-trivial behaviour of the critical boundary κ _c ($=1/√2 in bulk materials) between type-I and type-II phase transition at mesoscopic scales. Beyond the experimental-theoretical agreement, the question whether the GL model remains valid far below Tc is also addressed. The temperature dependence of the adjusted characteristic lengths is compared with different theoretical and empirical laws. The best agreement is achieved for the Gorter-Casimir two-fluid model. A comparison between lead nanowire arrays electrodeposited under constant and pulsed voltage conditions allows us to distinguish both samples in terms of their electronic mean free paths. The characterisation of the latter quantities concurs perfectly with the experimental expectation given the different electrodeposition techniques.