Graphene is a single layer of graphite with many unique mechanical, electrical, and optical properties. In addition, graphene is also known to adsorb wide range of biomolecules including single-stranded DNA. On the other hand, the adsorption of double-stranded DNA was much weaker. To properly disperse in water, graphene oxide (GO) is often used due to its oxygen-containing groups on the surface. Recently, it was discovered that it could efficiently quench the fluorescence of fluorophores that were adsorbed. With these properties, it is possible to prepare DNA-based optical sensors using GO. Majority of the DNA/GO-based fluorescent sensors reported so far were relied on the complete desorption of DNA probes. Even though all these reports demonstrated the sensitivity and selectivity of the system, the fundamentals of binding between DNA and GO were hardly addressed. Understanding and controlling binding between biomolecules and inorganic materials is very important in biosensor development. In this thesis, adsorption and desorption of DNA on the GO surface under different buffer conditions including ionic strength, pH, and temperature were systematically evaluated. For instance, adsorption is favored in a lower pH and a higher ionic strength buffer. It was found that once a DNA was adsorbed on the surface, little desorption occurred even in low salt buffers. Even with high pH or temperature, only small percentage of adsorbed DNA can be desorbed. To completely desorb the DNA, complementary DNA is required. The energies and activation energies associated with DNA adsorption/desorption were measured and molecular pictures of these processes were obtained. With the fundamental understanding of the DNA/GO interaction, we demonstrated that it is possible to achieve sensor regeneration without covalent immobilization. In addition, we also achieved the separation of double-stranded DNAs from single-stranded ones without using gel electrophoresis. We also studied the fluorescence property of DNA near the GO surface using covalently attached DNA probes. It was found that the fluorophore quantum yield and lifetime changed as a function of DNA length. This study is important for rational design of covalently linked DNA sensors. This study confirmed that fluorescence quenching by GO occurs in a distance-dependent manner. Energy transfer occurred between the fluorophore and GO to result in reduced quantum yield, shorter lifetime, and lower fluorescence intensity. Although fluorescent sensors based on covalently attached DNA probes on GO have not yet been reported, the study presented here clearly supported its feasibility.

Thesis (Ph. D.)--University of Texas at Austin, 2008. / Vita. Includes bibliographical references.

Graphene has grabbed enormous research attention due to its multiple unique properties. These properties, however, can be strongly influenced by lattice imperfections. Aberration corrected transmission electron microscopy (AC-TEM) is one of the leading methods to image two-dimensional materials at the atomic level. This thesis addresses the issue of structure and dynamics characterization of dislocations and grain boundaries (GBs) in graphene with single atom sensitivity using the state-of-the-art AC-TEM in Department of Materials, University of Oxford. My first goal is to understand the interaction between dislocation and the edge of graphene. When a dislocation is located near an edge, a decrease in the rippling and increase of the in-plane rotation occurs relative to the dislocations in the bulk. The increased in-plane rotation near the edge causes bond rotations at the edge of graphene to reduce the overall strain in the system. Dislocations are highly stable and remain fixed in their position even when located within a few lattice spacings from the graphene edge. With the aid of an in situ heating holder, the high temperature behavior of dislocations is then investigated. Control of temperature enables the differentiation of electron beam induced effects and thermally driven processes. An analysis of the dislocation movement shows both climb and glide processes, including new complex pathways for migration and large nanoscale rapid jumps between fixed positions in the lattice. The improved understanding of the high temperature dislocation movement provides insights into annealing processes in graphene and the behavior of defects with increased heat. The in situ heterogeneous nucleation and growth of graphene are also studied within the AC-TEM. The growth mechanism consists of alternating carbon cluster attachment and indentation filling to maintain a uniform growth front of lowest energy. The highly polycrystalline graphene seed is found to evolve with time into a higher order crystalline structure. The motion of GBs is discontinuous and mediated by both bond rotation and atom evaporation. These results provide insights into the formation of crystalline seed domains that are generated during bottom-up graphene synthesis. Finally, the formation, reconfiguration and annihilation of GB loops are demonstrated. It is shown that the GB loop cannot fully relaxed under electron beam irradiation with its terminal state being isolated dislocations far apart from each other. Line defects composed of several adjacent excess-atom defects can be found during the reconfiguration process. This work gives detailed information about the stability and behavior of large GB loops in two dimensional materials.

Photodetectors are essential in optoelectronics as they allow the conversion of optical signals into electrical outputs. Silicon, germanium and III-V semiconductors currently dominate the photodetector market. In this dissertation I exploit the potential of layered materials to demonstrate a class of photodetectors able to challenge existing technological issues. I first demonstrate a fabrication method for high-mobility, chemical-vapour-deposited graphene devices which could help to increase the responsivity in graphene-based photodetectors. I then show three examples of graphene-based Schottky photodetectors working at the telecommunication wavelength $\lambda$=1550nm, two for free-space illumination and one for on-chip applications. These are able to achieve responsivities up to 1A/W with relatively-low operation voltage (-3V), similar to those achieved with germanium. I then target the mid-infrared range ($\lambda\sim$10$\mu$m), where emission from objects at room temperature has a peak. I show graphene-based pyroelectric bolometers with temperature coefficient of resistance up to 900\%/K, two orders of magnitude higher compared to current solutions based on thin oxide membranes. I present flexible photodetectors working in the visible range ($\lambda$=642nm) with gate-tunable graphene/MoS$_2$ heterostructures and show responsivity up to 45A/W, 82\% transparency, and low voltage operation (-1V). The responsivity is two orders of magnitude higher compared to semiconducting flexible membranes. Graphene/MoS$_2$ photodetectors can be bent without loss in performance down to a bending radius of 1.4cm. I finally report on the investigation of superconducting properties of layered materials with the target of realizing ultra-sensitive superconducting photodetectors. Unconventional superconductivity is induced in graphene by proximity with a cuprate superconductor. I used gating to turn semiconducting, few-layer MoS$_2$ into a superconductor, which allowed us to unveil the presence of a multi-valley transport in the superconducting state. Electrical properties of the layered superconductor NbSe$_2$ are then studied. I then used NbSe$_2$ ultrathin flakes to realize superconducting photodetectors at $\lambda$=1550nm, reaching a sensitivity down to few thousand photons.

The paper discusses a two-step process for the simultaneous extraction of graphene quantum dots and chemicals. The two steps are sequential structure disruption by supercritical CO2 explosion followed by a low temperature (120oC), non-catalytic transfer hydrogenation in supercritical CO2. The key idea of this research is, one hydrogen atom from hydrogen transfer agent (HTA) one hydrogen atom from water is used to hydrogenate the coal. The use of supercritical CO2 enhances the rate of hydrogenation, helps in dissolution of non-polar molecules and removal from the reaction site. The coal dissolution products are polar and non-polar. A phase transfer agent (PTA) allows seamless transport of the ions and byproduct between the aqueous and organic phases. A polar modifier (PM) for CO2 has been added to aid in the dissolution and removal of the polar components. The effect of feed conditions on the liquefaction process has been investigated. The response metrics considered were the conversion of coal and the yields of various organic classes such as ketones, alkanes, alkenes, aliphatic acids, alcohols, amines, aromatics and aromatic oxygenates. Ketones were found to be the major constituent of the products. Graphene quantum dots were also extracted.

In this research work, we have investigated the band engineering of epitaxial graphene using first principles calculations. Epitaxial graphene on SiC (0001) surface is modified by using different methods such as intercalation, doping, passivation and oxidation. The calculations are done using Density functional theory which is implemented in quantum espresso package. In the presence of H intercalation, epitaxial graphene is shown to have p type behavior with monolayer graphene. However this behavior is different for multilayer epitaxial graphene systems, and it depended on the concentration of the H atoms. When epitaxial graphene is intercalated with Ge atoms, the Ge atoms make clusters and these clusters are responsible for the electronic properties of the epitaxial graphene systems. As a result of oxidation of epitaxial SiC surface, the graphene layer is mostly stable on the surface for both silicates and oxynitrides structures. For silicate/SiC configurations, the epitaxial graphene is shown to be less n type. For oxynitrides/ SiC configurations, epitaxial graphene is shown to be neutral. In the presence of oxygen intercalation with silicate/SiC, epitaxial graphene is shown to have p type behavior. These systematic studies of epitaxial graphene will opens up great potential for electronic applications. Additionally the resultant models can be used to guide further studies.

The discovery of monolayer graphene by Manchester group has led to intensive research into a variety of applications across different disciplines. As a monolayer of carbon atoms, graphene presents a high surface to volume ratio and a good electronic conductivity, making it sensitive to its surface bio-chemical environment. This project investigated the fabrication of electronic biosensors using different graphene-based materials. It included the production of graphene, the fabrication of electronic devices, the chemical functionalisation of graphene surface and the specific detection of target bio-molecules. This project first investigated the production of graphene using three different methods, namely mechanical exfoliation, physical vapour deposition and electrochemical reduction of graphene oxide. With respect to the physical vapour deposition method, the production of large area transfer-free graphene from sputtered carbon and metal layers on SiO2 substrate has, for the first time, been achieved. The relationship between growth parameters and the quality of resultant graphene layer has been systematically studied. In addition, a growth model based on the detailed analysis of morphological structures and properties of graphene film was simultaneously proposed. Optical microscopy, Raman spectroscopy and atomic force microscopy were used for the evaluation of the number, the quality and the morphology of resultant graphene layers in each method. To investigate the performance of graphene electronic devices, field effect transistors were fabricated using both exfoliated and chemical vapour deposited graphene. A novel technique for graphene patterning has been developed using deep ultraviolet baking and an improved photolithography method. A new shielding technique for the low damage deposition of Au electrodes on graphene has also been developed in this project. The practical challenges of device fabrication and performance optimisation, such as polymer residue and contact formation, have been studied using Raman spectroscopy and the Keithley 2602A multichannel source meter. For the functionalisation of graphene, a number of chemicals were investigated to provide linking groups that enable binding of bio-probes on the graphene surface. Hydrogen peroxide and potassium permanganate have been demonstrated to have the capability of immobilising oxygen-containing groups onto graphene. The levels of oxidation were estimated by energy dispersive analysis and Fourier transform infrared spectroscopy. In addition, aminopropyltriethoxysilanes and polyallylamine have exhibited good efficiency for immobilising amino groups onto graphene. The resultant graphene was characterised by X-ray photoelectron spectroscopy and cyclic voltammetry measurements. Graphene electrodes modified with electrochemically reduced graphene oxide were developed for the first time which exhibit significantly improved redox currents in electrochemical measurements. Using single stranded DNA immobilised via π-π bonds as probes, these electrodes showed a limit of detection of 1.58 x 10-13 M for the human immunodeficiency virus 1 gene. In parallel, human chorionic gonadotropin sensors were developed by immobilising its antibodies on 1-pyrenebutyric acid N-hydroxysuccinimide ester functionalised graphene field effect transistors. These field effect transistors have been demonstrated to exhibit a quantitative response toward the detection of 0.625 ng/ml antigen. In summary, the fabrications of two types of graphene-based biosensors for the detection of specific DNA sequence and human chorionic gonadotropin have been achieved in this project. Their sensitivity, selectivity, reproducibility and capability of multiple biomarker detection need to be further improved and explored in future work. The outcomes of this project have provided not only ready-made biosensing platforms for the detection beyond these two targets, but also novel techniques applicable to the development of multidisciplinary applications beyond biosensor itself.

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In this thesis, the growth mechanism of graphene on a transition metal support is determined, and the epitaxial relationship investigated. The main technique used is low- temperature scanning tunnelling microscopy (STM), which is introduced in Chapter 2. Epitaxial graphene synthesised on copper (foil and (110) single crystal), from the dehydrogenation of ethene, is investigated by STM and low energy electron diffraction (LEED) in Chapter 4. Despite the weak epitaxial relationship that exists, LEED uncovers two preferred orientations of the graphene over the copper. Further investigation reveals restructuring of the copper foil from a predominantly (100) orientation to (n10) facets. Structural feedback is found to exist, with the graphene growth inducing and stabilising faceting of the copper surface, and the facets in-turn playing an important role in the graphene growth mechanism. The preferred orientations, which are also seen on the single crystal, are most likely determined during nucleation and early stage growth, where it is expected that the interaction is stronger. The growth mechanism for the formation of graphene from ethene is studied on a Rh(111) surface in Chapter 5. This is found to consist of two regimes, with the first revolving around the transformation from aliphatic hydrocarbons to aromatic intermediates. This occurs through the decomposition and condensation of ethene, resulting in the formation of one-dimensional polyaromatic hydrocarbons (1D-PAHs). The second regime is characterised by the transition from these 1D-PAHs, to the 2D graphene. The previously produced 1D-PAHs, decompose to form size-selective carbon clusters, with these clusters being the precursors to graphene condensation. In Chapter 6, the conclusions of Chapter 5 are built upon through investigation into the effect of different hydrocarbon feedstocks on the graphene growth pathway. Benzene, tetracene, and perylene are the feedstocks examined. In all cases 1D-PAHs are formed, which decompose to clusters that subsequently condense to form graphene.