This thesis introduces a new strategy to fabricate single molecular transistor by utilizing the covalent chemistry to reconnect the molecule with the electroburnt graphene nanogap. We studied the effect of coupling chemistry and molecular length on the efficiency of reconnection between the molecule and the graphene. With this technique, we are also able to observe the Coulomb Blockade phenomenon, which is a characteristics of single-electron transistors. The high yield and versatility of this approach augur well for creating a new generation of sensors, switches, and other functional devices using graphene contacts. This thesis also introduces a new type of organic single-crystal p-n heterojunction inspired from the ball-and-socket shape-complementarity between fullerene and contorted dibenzotetrathienocoronene (c-DBTTC). We studied the influence of temperature, pressure, and time on the self-assembly process of contorted dibenzotetrathienocoronene on the as-grown fullerene crystals. We also utilized fluorescence microscopy to investigate the charge transfer in this type of p-n heterojunction. Finally, this thesis introduces one-dimensional and two-dimensional programming in solid-state materials from superatom macrocycles. We find that the linkers that bridges the two superatoms determine the distance and electronic coupling between the two superatoms in the macrocycle, which in turn determines the way they self-assembled in the solid-state materials. The thesis is composed of four chapters. The first chapter introduces why we are in terested in molecular transistors and new functional materials, and what has been done so far. The second chapter described the approach we developed to assemble single molecule into circuits with graphene electrodes. The third chapter details the method to fabricate the organic single-crystal C60-DBTTC p-n heterojunction, which is of great importance to understand their charge transfer process. The last chapter introduced a new series of superatom macrocycles and their self-assembly into solid-state materials with electron acceptor tetracyanoethylene.

An important goal of nanoscience is the self-assembly of nanoscale building blocks into complex nanostructures. DNA is an important and versatile building block for nanostructures because of its small size, predictable base pairing, and numerous sequence possibilities. I use DNA origami to design and fold DNA into predesigned shapes, to assemble thin, branched DNA nanostructures as templates for nanoscale metal features. Using a PCR-based scaffold strand generation procedure, several wire-like nanostructures with varying scaffold lengths were assembled. In addition, more complex prototype circuit element structures were designed and assembled, demonstrating the utility of this technique in creating complex templates. My fabrication method for DNA-templated nanodevices involves a combination of techniques, including: solution assembly of the DNA templates, surface orientation and placement, and selective nanoparticle attachment to form nanowires with designed gaps for the integration of semiconducting elements to incorporate transistor functionality. To demonstrate selective surface placement of DNA templates, DNA origami structures have been attached between gold nanospheres assembled into surface arrays. The DNA structures attached with high selectivity and density on the surfaces. In a similar base-pairing technique, 5 nm gold nanoparticles were aligned and attached to specific locations along DNA templates and then plated to form continuous metallic wires. The nanoparticles packed closely, through the use of a high density of short nucleotide attachment sequences (8 nucleotides), enabling a median gap size of 4.1 nm between neighboring nanoparticles. Several conditions, including hybridization time, magnesium ion concentration, ratio of nanoparticles to DNA origami, and age of the nanoparticle solution were explored to optimize the nanoparticle attachment process to enable thinner wires. These small, branched nanowires, along with the future addition of semiconducting elements, such as carbon nanotubes, could enable the formation of high-density self-assembled nanoscale electronic circuits.

Dynamic Kinetic Selection (DKS) suggests that kinetic, rather than thermodynamic, stability will dictate the composition of a replicating population of biomolecules. Here, the results obtained from a series of five related reactions involving gradually increasing percentages of randomly-mutated substrate fragments to generate variants of full-length Azoarcus group I intron through an autocatalytic self-assembly reaction involving a series of recombination events, showed DKS as a driving factor in dictating the population composition of full-length product assembled from substrates that had fewer positions available to randomization. In trying to elucidate a plausible scheme for the origins of complex biomolecules on the prebiotic Earth, the suggestion that networks comprised of interacting molecules were more likely to evolve into biomolecules capable of obtaining and sustaining characteristics attributed to living molecules has gained traction within the past few years. Of specific interest is the catalytic efficacy of ribozymes whose genotypes require that they interact with molecules of the same genotype (selfish systems) to be effective catalysts versus those that are more effective when accomplishing catalysis by cooperating with ribozymes of a different genotype (cooperative systems). Here, the Azoarcus I ribozyme was used to compare these two types of system. Both systems were shown to robustly produce full-length product. Two different methods of introducing random mutations into substrate fragments for the reactions described in this thesis were employed. The differences in the preparation methods for the substrates was not expected to have an impact on the nature of the full-length product. However, there was no correlation between the positions that tended to be more tolerant of accepting random mutations between the products arising from the two preparation methods. One preparation method yielded full-length ribozymes more consistent with the secondary structure of the wild-type ribozyme and followed substitution patterns found in in vivo nucleic acid substitutions, whereas the other method provided full-length ribozymes that tolerated mutations that would be expected to greatly affect the secondary structure of the ribozyme and those positions tended to mutate evenly to any of the three possible alternative nucleobases. Point mutations introduced into ribozyme substrate fragments may have a deleterious, neutral, or beneficial effect, depending on their impact on the catalytic capability of the molecule vis-á-vis the effect, if any, the change has to the secondary and tertiary structure of the ribozyme. In this dissertation, the results of two series of point mutation reactions are addressed. The first set showed a point mutation to have a deleterious effect, whereas concerted mutations did not significantly affect activity of the ribozyme. The second series of reactions involved point mutations at a position that had previously been determined to be highly tolerant of random mutations. Results suggested that substitutions at this position had a minimal impact on ribozyme activity.

Designing self-assembling DNA nanostructures often requires the identification of a route for a scaffolding strand of DNA through the target structure. When the target structure is modeled as a graph, these scaffolding routes correspond to Eulerian circuits subject to turning restrictions imposed by physical constraints on the strands of DNA. Existence of such Eulerian circuits is an NP-hard problem, which can be approached by adapting solutions to a version of the Traveling Salesperson Problem. However, the author and collaborators have demonstrated that even Eulerian circuits obeying these turning restrictions are not necessarily feasible as scaffolding routes by giving examples of nontrivially knotted circuits which cannot be traced by the unknotted scaffolding strand. Often, targets of DNA nanostructure self-assembly are modeled as graphs embedded on surfaces in space. In this case, Eulerian circuits obeying the turning restrictions correspond to A-trails, circuits which turn immediately left or right at each vertex. In any graph embedded on the sphere, all A-trails are unknotted regardless of the embedding of the sphere in space. We show that this does not hold in general for graphs on the torus. However, we show this property does hold for checkerboard-colorable graphs on the torus, that is, those graphs whose faces can be properly 2-colored, and provide a partial converse to this result. As a consequence, we characterize (with one exceptional family) regular triangulations of the torus containing unknotted A-trails. By developing a theory of sums of A-trails, we lift constructions from the torus to arbitrary n-tori, and by generalizing our work on A-trails to smooth circuit decompositions, we construct all torus links and certain sums of torus links from circuit decompositions of rectangular torus grids. Graphs embedded on surfaces are equivalent to ribbon graphs, which are particularly well-suited to modeling DNA nanostructures, as their boundary components correspond to strands of DNA and their twisted ribbons correspond to double-helices. Every ribbon graph has a corresponding delta-matroid, a combinatorial object encoding the structure of the ribbon-graph's spanning quasi-trees (substructures having exactly one boundary component). We show that interlacement with respect to quasi-trees can be generalized to delta-matroids, and use the resulting structure on delta-matroids to provide feasible-set expansions for a family of delta-matroid polynomials, both recovering well-known expansions of this type (such as the spanning-tree expansion of the Tutte polynnomial) as well as providing several previously unknown expansions. Among these are expansions for the transition polynomial, a version of which has been used to study DNA nanostructure self-assembly, and the interlace polynomial, which solves a problem in DNA recombination.

This thesis outlines a study of the physical changes that hybridisation imposes on single-stranded DNA (ssDNA) immobilised by one end to a substrate, and of how such physical changes can be exploited to detect specific sequences of DNA in a target solution. The system studied was composed of a mixed monolayer of 20mer ssDNA with C6 alkanethiolate modifications on their 3??? ends and short-chain hydroxyterminated alkanethiolates, on a gold substrate. It was prepared using the self-assembly properties of alkanethiols on gold. Atomic force microscopy images showed that the end-immobilised ssDNA is flexible enough to lie over the diluent hydroxy-terminated self-assembled monolayer (SAM). Hybridisation was shown to cause the DNA to become more rigid and stand up off the substrate due to an increase in persistence length. Such physical changes of the DNA upon hybridisation were significant enough to be exploited in the development of a DNA recognition interface. The recognition interface was designed with the view of keeping it both simple to make and simple to use, and was coupled with electrochemical transduction. A label-free recognition interface was developed that relied on the oxidation of the sulfur head group of the alkanethiolate SAM to detect hybridisation (firstly air oxidation and then electrochemical oxidation). It produced a positive signal upon hybridisation with complementary target DNA. Improvements in the reliability and robustness of the recognition interface were made using a labelled approach. The labelled version employed electroactive molecules as labels on the 5??? ends of the probe DNA strands. Two labels were investigated ??? anthraquinone and ferrocene. The flexibility of the ssDNA ensured that the redox labels were able to directly access the underlying gold electrode. Hybridisation was expected to remove the labels from the electrode due to an increase in the DNA???s persistence length, and thus perturb the electrochemical signal. The use of ferrocene as a label provided a ???proof-of-concept??? for the system. The labelled recognition interface provides a foundation for the future development of a simple, reliable, and selective DNA hybridisation biosensor.

The adsorbed layer morphology of a series of surfactants under different conditions has been examined primarily using atomic force microscopy (AFM). The morphologies of single and double chained quaternary ammonium surfactants adsorbed to mica have been characterised using AFM at concentrations below the cmc. Mixing these different types of surfactants systematically allowed a detailed examination of the change in adsorbed film curvature from the least curved bilayers through to most curved globules. From this study a novel mesh structure was discovered at curvatures intermediate to bilayers and rods. A mesh was again observed in studies examining the morphology change of adsorbed nonionic surfactant films on silica with variation in temperature. Other surfactant mixtures were also examined including grafting non-adsorbing nonionic surfactants and diblock copolymers into quaternary ammonium surfactant films of different morphologies.

<p>Today, the dominating way of patterning nanosystems is by irradiation-based lithography (e-beam, DUV, EUV, and ions). Compared to the other irradiations, ion tracks created by swift heavy ions in matter give the highest contrast, and its inelastic scattering facilitate minute widening and high aspect ratios (up to several thousands). Combining this with high resolution masks it may have potential as lithography technology for nanotechnology. Even if this ‘ion track lithography’ would not give a higher resolution than the others, it still can pattern otherwise irradiation insensitive materials, and enabling direct lithographic patterning of relevant material properties without further processing. In this thesis ion tracks in thin films of polyimide, amorphous SiO₂ and crystalline TiO₂ were made. Nanopores were used as templates for electrodeposition of nanowires.</p><p>In lithography patterns are defined by masks. To write a nanopattern onto masks e-beam lithography is used. It is time-consuming since the pattern is written serially, point by point. An alternative approach is to use self-assembled patterns. In these first demonstrations of ion track lithography for micro and nanopatterning, self-assembly masks of silica microspheres and porous alumina membranes (PAM) have been used. </p><p>For pattern transfer, different heavy ions were used with energies of several MeV at different fluences. The patterns were transferred to SiO₂ and TiO₂. From an ordered PAM with pores of 70 nm in diameter and 100 nm inter-pore distances, the transferred, ordered patterns had 355 nm deep pores of 77 nm diameter for SiO₂and 70 nm in diameter and 1,100 nm deep for TiO₂. The TiO₂ substrate was also irradiated through ordered silica microspheres, yielding different patterns depending on the configuration of the silica ball layers. </p><p>Finally, swift heavy ion irradiation with high fluence (above 10¹⁵/cm²) was assisting carbon nanopillars deposition in a PAM used as template. </p>

This paper presents a new technique for the monolithic heterogeneous integration of compound semiconductor devices with silicon integrated circuits, and establishes the theoretical foundation for a key element of the process, tailored magnetic attraction and retention. It is shown how a patterned thin film of hard magnetic material can be used to engineer the attraction between the film and nanopills covered with a soft magnetic material. With a suitable choice of pattern, it is anticipated that it will be possible to achieve complete filling of recesses in the surface of fully-processed integrated circuit wafers, preparatory to subsequent processing to fabricate the nanopills into heterostructure devices integrated monolithically with the pre-existing electronics. / Singapore-MIT Alliance (SMA)

Colloidal self assembly is an efficient method for making 3-D ordered nanostructures suitable for materials such as photonic crystals and macroscopic solids for catalysis and sensor applications. Colloidal crystals grown by convective methods exhibit defects on two different scales. Macro defects such as cracks and void bands originate from the dynamics of meniscus motion during colloidal crystal growth while micro defects like vacancies, dislocation and stacking faults are indigenous to the colloidal crystalline structure. This paper analyses the crystallography and energetics of the microscopic defects from the point of view of classical thermodynamics and discusses the strategy for the control of the macroscopic defects through optimization of the liquid-vapor interface. / Singapore-MIT Alliance (SMA)

Thesis (Ph. D.)--University of Oregon, 2006. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 173-182). Also available for download via the World Wide Web; free to University of Oregon users.