published_or_final_version / Physics / Master / Master of Philosophy

published_or_final_version / abstract / Physics / Master / Master of Philosophy

published_or_final_version / abstract / Physics / Master / Master of Philosophy

published_or_final_version / abstract / Physics / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Physics / Doctoral / Doctor of Philosophy

published_or_final_version / Physics / Doctoral / Doctor of Philosophy

No description available.

This thesis investigates ways in which a nanoscale production line may be built from synthetic DNA components. One property of a production line is motion, the coordinated movement of components, in this case strands of DNA, between specific locations. Another property is the ability to assemble a product, where smaller molecular building blocks are attached to D A and react when brought together by the DNA assembly line. An important fea- ture of either task is the ability of the mechanism to proceed with minimum user interaction: it is preferable that the assembly line be autonomous. The challenges and design principles of molecular machines working in nano- scale environments are first considered. Previous studies demonstrating the use of synthetic DNA not only as a self-assembling material to build nano- structures, but also to coordinate motion, are summarized. All DNA nano- machines that operate through the exchange of DNA strands are coordinated by toeholds. A 'split toehold', one that combines two smaller toeholds on distal sections of DNA held in proximity, is proposed as a way to allow a single cargo strand to interact with many different components. A molecular motor is then developed that transports a cargo between track locations. The fuel strands are hairpins, that carry instructions directing the cargo to the next anchorage. The switching of cargo direction in response to the chemical environment is also investigated. Two mechanisms that may allow the autonomous assembly of components are investigated, one of which is demonstrated using DNA-linked cleavable molecular building blocks. Further extensions to the mechanism are investi- gated, for example, the ability to use the DNA mechanism itself as a barcode containing information on the order of assembled ingredients.

DNA origami is a method for constructing 2-dimensional nanostructures with arbitrary shapes, by folding a long piece of viral genomic DNA into an extended pattern (Rothemund, 2006). In this thesis DNA origami nanostructures that in- corporate active transport are developed, by combining rectangular DNA origami tiles with either synthetic DNA motors, or the protein motor F1-ATPase. The transport of an autonomous, unidirectional, and processive 'burnt-bridges' DNA motor across an extended linear track anchored to a DNA origami tile is demonstrated. Ensemble fluorescence measurements are used to characterise motor transport, and are compared to a simple deterministic model of stepping. The motor moves 100 nm along a track at 0.1 nms-1 Atomic force microscopy (AFM) is used to study the transport of individual motor molecules along the track with single-step resolution. A DNA origami track for a 'two-foot' DNA motor is also developed, and is characterised by AFM and ensemble fluorescence measurements. The burnt-bridges DNA motor is then directed through a track network with either 1 or 3 bifurcations. Ensemble fluorescence measurements demonstrate that the path taken can be controlled by the addition of external control strands, or pre-programmed into the motor. A method for attaching the rotary motor protein F1-ATPase to DNA origami tiles is developed. Different bulk and single-molecule methods for demonstrat- ing protein binding are explored. Single-molecule observations of rotation of the protein motor on a DNA origami substrate are made, and are of equivalent data quality to existing techniques.

A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of PhD. August 9, 2017 / Nano-structured carbon lms, long studied due to the promise of exceptional quantum transport properties, present a signi cant problem in condensed matter due to the disorder which inherently forms in these materials. This work addresses the role of structural disorder in low dimensional carbon systems. The in uence of structural disorder on resonant transmission is studied in diamond-like carbon superlattices. Having established a model for disorder, this model for the structural changes is then applied to interpret experimental measurements of diamond-like carbon superlattices. The role of phonons on resonant transmission under a high frequency gate potential was also studied. This model for structural disorder in heterogeneous carbon lms was then applied to disordered superconductors close to the Anderson-Mott transition using the inhomogeneous Bogoliubov-de Gennes theory. This analysis is then used in support of experimental work to understand the superconductor-insulator transition in boron doped nano-crystalline diamond lms. Coherent quantum transport e ects were demonstrated in structurally-disordered diamondlike carbon (DLC) superlattices through distinct current modulation (step-like features) with negative differential resistance in the current-voltage (I-V) measurements. A model for these structurally disordered superlattices was developed using tight-binding calculations within the Landauer-B uttiker formalism assuming a random variation of the hopping integral following a Gaussian distribution. Calculations of the I-V characteristics for different con gurations of superlattices compliment the interpretation of the measured I-V characteristics and illustrate that while these DLC superlattice structures do not behave like conventional superlattices, the present model can be used to tailor the properties of future devices. Furthermore this tandem theoretical and experimental analysis establishes the validity of the model for structural disorder. The same model for the variation of disorder was then applied to interpret the electronic transport properties of disordered graphene-like carbon thin films. The influence of disorder on the activation energy in few layer graphitic lms was modelled and compared with experimental observations through collaboration. The lms, grown by laser ablation, allowed the speci c e ects of structural disorder in the sp2 - C phase to be probed. Defects acted as effective barriers resulting in localization of charge carriers. Electron transmission spectra, calculated with a tight-binding model, accounted for the change of localization length as a result of disorder in the sp2 - C phase. This theoretical study showed that the localization length of the thin graphitic lms can be tuned with the level of disorder and was shown to be consistent with experimental studies. The in uence of nitrogen incorporation on resonant transmission in DLC superlattices was then studied theoretically. This study illuminated the speci c role of the nitrogen potential in relation to the Fermi level (EF ) in nitrogen incorporated amorphous carbon (a- CN) superlattice structures. In a-CN systems, the variation of conductivity with nitrogen percentage has been found to be strongly non-linear due to the change of disorder level. The e ect of correlated carbon and nitrogen disorder was investigated in conjunction with the nitrogen potential through analysis of transmission spectra, calculated using a tight binding model, which showed two broad peaks related to these species. It was shown that the characteristic transmission time through nitrogen centres can be controlled through a combination of the nitrogen potential and correlated disorder. In particular, by controlling the arrangement of the nitrogen sites within the sp2 - C clusters as well as their energetic position relative to EF , a crossover of the pronounced transmission peaks of nitrogen and carbon sites can be achieved. Furthermore, it was shown that nitrogen incorporated as a potential barrier can also enhance the transmission in the a-CN superlattice structures. The strong non-linear variation of resistance and the characteristic time of the structures can explain the transport features observed experimentally in a-CN fi lms. This analysis was then partnered with measurements performed on nitrogen-incorporated carbon superlattices (N-DLC QSL) by Neeraj Dwivedi (National University of Singapore). The electrical characteristics of these nitrogen incorporated superlattice devices revealed prominent negative di erential resistance (NDR) behavior. The interpretation of these measurements was supported by 1D tight binding calculations of disordered superlattice structures (chains), which included signi cant bond alternation in sp3-hybridized regions. This analysis showed improved resonant transmission, which can be ascribed to nitrogendriven structural modi cation of the N-DLC QSL structures, especially the increased sp2-C clustering that provides additional conduction paths throughout the network. In order to determine the in uence of additional factors on coherent quantum states in molecular systems as an extension to the analysis on superlattices, a theoretical study of the electron-phonon interaction in double barrier structures under the in uence of a timedependent gate potential was undertaken. The Floquet theory was employed along with expansion in a polaron eigenbasis to render a multi-dimensional single body problem. An essentially exact solution was found using the Riccati matrix technique. It was demonstrated that optimal transmission can be achieved by varying the frequency of the gate potential. In addition, it was shown that the gate potential can be used to control the energy of the resonant states very precisely while maintaining optimal transmission. Having gained a deep understanding of the structural changes induced in carbon systems through the incorporation of nitrogen, a similar structural model was then applied to study the changes induced in diamond and nanocrystalline fi lms by boron incorpora- tion. Boron doped diamond provides an interesting superconductor with ongoing debate surrounding the nature of the impurity band and the effect on the superconducting phase transition of structural changes induced by boron incorporation. The in uence of disorder, both structural (non-diagonal) and on-site (diagonal), was studied through the inhomogeneous Bogoliubov-de Gennes (BdG) theory in narrow-band disordered superconductors with a view towards understanding superconductivity in boron doped diamond (BDD) and boron-doped nanocrystalline diamond (B-NCD) lms. We employed the attractive Hubbard model within the mean eld approximation, including a short range Coulomb interaction between holes in the narrow acceptor band. We studied substitutional boron incorporation in a triangular lattice, with disorder in the form of random potential uctuations at the boron sites. The role of structural disorder was investigated through non-uniform variation of the tight-binding coupling parameter where, following experimental ndings in BDD and B-NCD lms, we incorporated the concurrent increase in structural disorder with increasing boron concentration. Stark differences between the ffects of structural and on-site disorder were demonstrated and showed that structural disorder has a much greater e ect on the density of states, mean pairing amplitude and super uid density than on-site potential disorder. We showed that structural disorder can increase the mean pairing amplitude while the spectral gap in the density of states decreases, with states eventually appearing within the spectral gap for high levels of disorder. This study illustrated how the effects of structural disorder can explain some of the features found in superconducting BDD and B-NCD lms, such as a tendency towards saturation of the critical temperature (Tc) with boron doping and deviations from the expected Bardeen-Cooper-Shrie er (BCS) theory in the temperature dependence of the pairing amplitude and spectral gap. The variation of the super uid density considering only structural disorder was markedly different from the variation with on-site disorder only and revealed that structural disorder is far more detrimental to superconductivity and accounts for the relatively low Tc of BDD and B-NCD in comparison to the Tc predicted using the conventional BCS theory. This theoretical work was then used to interpret features in the measured transport properties of B-NCD lms with di erent doping concentrations and microstructures. The temperature dependence of a distinct local maximum in eld dependent magnetoresistance measurements showed suppression of the density of states as the system breaks up into superconducting regions separated by grain boundaries. Differential resistance measurements at different temperatures and magnetic fi elds showed a transition from a local minimum at zero applied current, indicative of persisting superconducting regions, to a local maximum. A power law dependence over a certain current range in the measured I-V characteristics at di erent magnetic elds suggests a Berezinski-Kosterlitz-Thouless (BKT) transition. In addition, features in the magnetoresistance clearly indicate additional phases. Together with features in current-voltage measurements, these signatures show the coexistence of superconductivity and additional competing phases close to the Anderson-Mott transition. / LG2018