Gene regulation is vital to the success of all living organisms. Understanding this complex process is crucial to our knowledge of how cells function and how in some cases they can lead to debilitating or even fatal disease. In this thesis I focus on a set of DNA-binding proteins known as transcription factors (TFs), proteins fundamental to the process of gene regulation at the level of transcription. I develop assays and techniques for the detection and quantitation of TFs in vitro and in vivo as well as a method for TF encapsulation and release. The advantages of the TF detection assays in this thesis are made possible through the use of single-molecule (sm) fluorescence. This methodology enables detection of individually labeled molecules allowing discrimination of sample heterogeneities inaccessible with ensemble techniques. Here I present two different TF assays based on two sm observables: relative probe stoichiometry and Förster resonance energy transfer (FRET). The first assay design, based on stoichiometry, detects TFs using TF-dependent coincidence of two distinctly labelled DNA ‘half-sites’. I demonstrate sensitive detection (~ pM) in solution and on surfaces, multiplexed detection of multiple TFs, and detection in cell lysates. A kinetic model of the system is also developed, verified experimentally and used to quantify TF concentrations without the need for a calibration curve. The second assay design, based on FRET, is a novel approach to TF detection using TFmediated DNA bending. TFs are detected by bending the sensor and monitored with FRET at the single-molecule or ensemble level. I demonstrate TF detection in purifed form and expressed in cell lysates. As this sensor was designed for use in vivo, methods to hinder nuclease degradation are explored. For TF detection in vivo, I describe a successful strategy to internalise fluorescently labeled molecules into live E.coli. Viability and internalisation efficiency are characterised and ensemble measurements with FRET standards are demonstrated. Importantly, sm FRET measurements in vivo are achieved opening many exciting possibilities. The FRET based TF sensor is then internalised as a step towards real-time in vivo monitoring of TF concentrations. Finally a system based on DNA nanotechnology is presented for the non-covalent encapsulation and release of TFs. Such a system could be delivered into a cell to alter levels of gene expression using external stimuli as inputs. We believe these tools will generate valuable information in the study of prokaryotic gene expression as well as providing a potential commercial avenue towards diagnostics.

In this thesis, two-dimensional materials such as graphene are tested for their suitability for opto-electronic applications using terahertz time domain spectroscopy (THz-TDS). This ultrafast all-optical technique can probe the response of novel materials to photoexcitation, and yield information about the dynamics of the material systems. Graphene grown by chemical vapour deposition (CVD) is studied using optical-pump THz-probe time domain spectroscopy in a variety of gaseous environments in Chapter 4. The photoconductivity response of graphene grown by CVD is found to vary dramatically depending on which atmospheric gases are present. Adsorption of these gases can open a local bandgap in the material, allowing stimulated emission of THz radiation across the gap. Semiconducting equivalents to graphene, molybdenum disulphide (MoS₂) and tungsten diselenide (WSe₂), grown by CVD, are investigated in Chapter 5. These members of the transition metal dichalcogenide family show sub-picosecond responses to photoexcitation, suggesting promise for use in high-speed THz devices. In Chapter 6, an alternative production route to CVD is studied. Liquid-phase exfoliation offers fast, easy production of few-layer materials. THz spectroscopy reveals that the dynamics of these materials after photoexcitation are remarkably similar to those in CVD-grown materials, offering the potential of cheaper materials for future devices. Finally in Chapter 7, it is shown that carbon nanotubes can be used to make ultrafast THz devices. Unaligned, semiconducting single walled carbon nanotubes can be photoexcited to produce an ultrafast, dynamic THz polariser. The work in this thesis demonstrates the potential for these novel materials in future opto-electronic applications. THz spectroscopy is shown to be an important tool for the characterisation of new materials, providing information that can be used to understand the dynamics of materials, and improve production methods.

Various synthetic methods have been developed to produce metal nanostructures including copper and iron nanostructures. Modification of nanoparticle surface to enhance their characteristic properties through surface functionalization with organic ligands ranging from small molecules to polymeric materials including organic semiconducting polymers is a key interest in nanoscience. However, most of the synthetic methods developed in the past depend widely on non-aqueous solvents, toxic reducing agents, and high temperature and high-pressure conditions. Therefore, to produce metal nanostructures and their nanocomposites with a simpler and greener method is indeed necessary and desirable for their nano-scale applications. Hence the objective of this thesis work is to develop an environmentally friendly synthesis method to make welldefined copper and iron nanostructures on a large-scale. The size and shape-dependent optical properties, solid-state crystal packing, and morphologies of nanostructures have been evaluated with respect to various experimental parameters. Nanostructures of copper and iron were prepared by developing an aqueous phase chemical reduction method from copper(II) chloride and Fe(III) chloride hexahydrate upon reduction using a mild reducing agent, sodium borohydride, under an inert atmosphere at room temperature. Well-defined copper nanocubes with an average edge length of 100±35 nm and iron nanochains with an average chain length up to 1.70 μm were prepared. The effect of the molar ratios of each precursor to the reducing agent, reaction time, and addition rate of the reducing agent were also evaluated in order to develop an optimized synthesis method for synthesis of these nanostructures. UV-visible spectral traces and X-ray powder diffraction traces were obtained to confirm the successful preparation of both nanostructrues. The synthesis method developed here was further modified to make poly(3-hexylthiophene) coated iron nanocomposites by surface functionalization with poly(3-hexylthiophene) carboxylate anion. Since these nanostructrues and nanocomposites have the ability to disperse in both aqueous-based solvents and organic solvents, the synthesis method provides opportunities to apply these metal nanostructures on a variety of surfaces using solution based fabrication techniques such as spin coating and spray coating methods.

Structural and optical properties of ZnO nanostructures synthesized by low energy ion implantation technique were examined. ZnO molecular ions were implanted into Si/SiO2 substrates at room temperature and then furnace annealed under different temperatures and environments. In all as-implanted samples only Zn nanostructures with varying diameters distributed into the Si/SiO2 matrices were observed. No trace of ZnO was found. The distributions of Zn nanostructures in Si/SiO2 closely matched results from Stopping and Range of Ions in Matter (SRIM) simulations. During annealing at 750 oC, Zn diffused both toward and away from the surface of the substrate and combine with oxygen to form ZnO nanostructures. At higher annealing temperatures ZnO bonding started to break down and transfer to zinc silicate (Zn2SiO4), and at 900 oC the ZnO was completely converted into Zn2SiO4. The average sizes of Zn/ZnO nanostructures depended on the ion fluence. If the fluence increased the average sizes of nanostructures also increased and vice versa. For room temperature photoluminescence (RT-PL), band-edge emission in the ultraviolet (UV) region was observed from all samples annealed at 700 oC/750 oC and were slightly blue shifted as compare to bulk ZnO. Donor-bound exciton (D,X) and acceptor-bound exciton (A,X) transitions were observed in low temperature photoluminescence (PL). The lifetime of both donor-bound excitonic emission (D, X) and acceptor-bound excitonic emission (A, X) were found to be in the picosecond (ps) range.

Low dimensional nanostructures of zinc oxide (ZnO), cupric oxide (CuO), and their composite nanostructures possess remarkable physical and chemical properties. Fundamental understanding and manipulation of these unique properties are crucial for all potential applications. Integration of nanostructured ZnO and CuO and their hybrid composites may play a significant role in the existing technology while paving the way for new exciting areas. Solution based low temperature synthesis of ZnO and CuO nanostructures have attracted extensive research efforts during the last decade. These efforts resulted in a plenteous number of nanostructures ranging from quantum dots into very complex three dimensional nanomaterials. Among the various low temperature synthesis methods the hydrothermal technique became one of the most popular approaches. The use of hydrothermal approach enabled the synthesis of diversity of nanomaterials on conventional and nonconventional substrates such as metals, glass, plastic and paper etc. The primary objectives of this thesis are to study and understand the characteristics of nanostructured ZnO, CuO, and their hybrid composites synthesized at low temperature. Likewise, the hybrid composites were successfully utilized to fabricate light emitting diodes and sensors. This thesis is organized into three major parts. In the beginning the synthesis and characterization of nanostructured ZnO, CuO, and their composite nanostructures are elaborated. Efforts have been made to understand the selective assembly of hierarchical CuO nanostructures on ZnO nanorods and to correlate it to the observed unique properties of the CuO/ZnO composite nanostructures. In the second part of the thesis fabrication, characterization, and device application of ZnO/p-polymer hybrid light emitting diode (HyLEDs) on flexible substrates are presented. In particular single and blended p-type light emissive polymers were controllably developed for potential greener and cheaper white light emitters. It was found that the HyLEDs exhibited rectifying diode characteristics together with white light emission covering the entire visible range. In the third part, pH and relative humidity sensing applications of CuO nanoflowers, and CuO/ZnO nanocorals, respectively, are described. A pH sensor based on CuO nanoflowers demonstrated good sensitivity and reproducibility over a wide range of pH. By taking the advantages of the selective growth of CuO nanostructures on ZnO nanorods and their naturally formed p-n heterojunction the realization of high sensitivity humidity sensor was achieved. The humidity sensor fabricated from the CuO/ZnO nanocorals displayed the highest sensitivity factor reported so far for its constituent materials; along with reasonably fast dynamic responses. A brief outlook into future challenges and opportunities are also presented in the last part of the thesis. / Nanophotonics

This thesis studies the application of silver nanowire transparent conductors in PbS quantum dot photovoltaics. Silver nanowires were synthesized using a colloidal method and characterized using scanning electron microscopy. Nanowires were deposited on glass substrates by a stamp transfer process to generate a low density continuous network of conductive nanowires. This resulted in a highly conductive and transparent film appropriate for optoelectronic applications. Nanowire synthesis, deposition, and processing were optimised to produce transparent conductors suitable for thin film photovoltaics. These nanowire films were used to fabricate lead sulphide (PbS) colloidal quantum dot solar cells. In this structure, p-type PbS quantum dots form a junction with a n-type ZnO nanoparticle layer. A variety of fabrication and processing treatments were developed in order to reduce short-circuiting of devices and to enhance cell performance. Moderate nanowire density, improved ZnO adherence, slight device aging, and increased PbS film thickness proved to result in the highest quality devices. The champion device developed in this thesis achieved a power conversion efficiency of 2.2%.

Semiconductors provide an interesting platform for studying light-matter interactions due to their unique electrically conductive behavior which can be deliberately altered in useful ways with the controlled introduction of confinement and doping, which changes the electronic band structure. This area of research has led to many important fundamental scientific discoveries that have in turn spawned a plethora of applications in areas such as photonics, microscopy, single-photon sources, and metamaterials. Silicon is the prevalent semiconductor platform for microelectronics because of its cost and electrical properties, while III-V materials are optimal for optoelectronics because of the ability to engineer a direct bandgap and create versatile heterojunctions by growing binary, ternary, or quaternary compounds.

[pt] A combinação de alta densidade, locais seletivos de nucleação e controle da distribuição de tamanho de nanoestruturas semicondutoras tem acelerado o desenvolvimento de dispositivos ópticos e eletrônicos. Para construir estruturas satisfazendo essas necessidades, várias combinações de técnicas deposição de pontos quânticos e nanolitografia foram desenvolvidas. A nanolitografia por AFM foi aplicada em diversos materiais abrindo uma possibilidade para fabricar dispositivos opto-eletrônicos.Nesta tese de Doutorado, apresentamos um estudo sistemático de crescimento de nanoestruturas de InAs em buracos produzidos na superfície (100) de substratos de InP por nanoindentação com o AFM. Para isto, a ponta precisa exercer uma força no InP que produz deformações plásticas na superfície. A pressão aplicada entre a extremidade da ponta de AFM e a superfície da amostra pode ser variada de modo controlado através do ajuste de alguns parâmetros operacionais do microscópio tais como setpoint, raio da ponta e constante de mola do cantilever. A habilidade para controlar a forma do padrão indentado assim como a natureza dos defeitos cristalinos permite controlar o crescimento seletivo de InAs por epitaxia em fase de vapor de metais orgânicos. Também é apresentada a fabricação de nanoestruturas de InAs/InP alinhadas em uma dimensão. A nanoindentação é produzida pelo arraste da ponta do AFM sob força constante ao longo das direções <100> e <110> do InP. Observamos que o número e o tamanho das nanoestruturas nucleadas são dependentes da distância entre as linhas litografadas. Esses resultados sugerem que o mecanismo de crescimento das nanoestruturas de InAs não é governado por degraus atômicos gerados durante a indentação. Os dados sugerem que, a densidade de defeitos induzidos mecanicamente, tais como discordâncias e fraturas, é o responsável pelo número de nanoestruturas nucleadas. / [en] The combination of high density, site selective nucleation, and size distribution control of semiconductor nanostructures has become a challenge in the development of effective optical and electronic devices. In order to build structures satisfying these requirements, various combinations of quantum dot deposition and nanolithography techniques have been developed. The AFM nanolithography technique has been applied on several materials opening a possibility to fabricate opto-electronic devices. In this Phd Thesis, we present a systematic study of growth of InAs nanostructures on pits produced on (100) InP by nanoindentation with the AFM. For that purpose, the AFM tip needs to exert a force on the InP that produces plastic deformation on the surface. The applied pressure between the very end of the AFM tip and the sample surface may be varied in a controlled way by adjusting some of the microscope operational parameters like set point, tip radius and cantilever normal bending constant. The ability to control the shape of the indentation pattern as well as the nature of the crystalline defects allows control of the selective growth of InAs by metal organic vapor phase epitaxy. We also report the fabrication of one-dimensional arrays of InAs/InP nanostructures. The nanoindentation is produced by dragging the AFM tip under constant force of the substrate, along the <100> and <110> InP crystallographic directions. We have observed that the number and the size of nucleated nanostructures are dependent on the distance between the lithographed lines. These results suggest that the growth mechanism of the InAs nanostructures on the pits produced by AFM on InP is not governed by the number of atomic steps generated during the scratching. Instead, the data suggests that, the density of mechanically induced defects, like dislocations and cracks, are responsible for the number of nucleated nanostructures.

The presented project explores the optical properties of magnetoplasmonic Au/Ni core-shell structures. The work aims at controlling dimensions and parameters in order to influence and analyze the optical properties of the nanostructures. The softwares utilized for the simulations were COMSOL Multiphysics 5.1 and MATLAB. Experimental results were acquired from labs done at Ångströms laboratory. From the research based study where the gold to nickel ratio was influenced, it was observed that the transmissions for the nanostructures at the differing wavelengths produced transmissions of similar bearings. Modes for certain wavelengths were found in correspondence with the transmissions and could potentially render explanations for influence on the optical properties of the nanostructures. Conclusively, it can be stated that the optical properties of the nanostructures could be influenced and controlled by varying the dimensions and properties of the said structure. Differing dimensions corresponded to noteworthy changes in the cross sections, the transmissions as well as the mode formations.

Na primeira parte desta dissertação, nos concentramos na utilização de uma abordagem baseada na remoção oxidativa controlada de sementes/núcleos promovida pela adição de HCl na síntese poliol de nanofios de prata (Ag). Isto possibilitou um controle fino sobre a espessura dos nanofios gerados na faixa de de 65 a 765 nm, no qual as larguras obtidos apresentaram um aumento linear em função do aumento na concentração de HCl utilizado na reacção. Embora a largura também se mostrou dependente de outros parâmetros experimentais, tais como a concentração de AgNO3 e polivinilpirrolidona (PVP) e temperatura, remoção oxidativa promovida por HCl possibilitou o controle sobre uma faixa de tamanhos mais ampla. Também investigamos as propriedades ópticas dos nanofios de Ag em função do seu tamanho e sua aplicabilidade como substratos para detecção atraves do fenômeno de espalhamento Raman intensificado por superfície (SERS). Na segunda parte deste trabalho, nanotubos de Ag-Au, Ag-Pt e Ag-Pd contendo morfologias de superfície controladas foram obtidos através da reação de substituicão galvânica entre os nanofios de Ag e íons AuCl4-, PtCl62-, e PdCl42-, respectivamente. Nesse caso, superfícies lisas foram obtidas a 100 oC enquanto superfícies rugosas foram observadas a temperatura ambiente. Mostramos ainda que superfícies lisas também puderam ser obtidas usando-se uma solução saturada de NaCl como solvente durante a reação galvânica. Na terceira parte deste trabalho, investigamos o efeito da excitação da ressonância plasmônica de superfície (SPR) nos nanofios de Ag sobre a atividade catalítica frente a redução do 4-nitrofenol. Contudo, nossos resultados mostraram um queda da atividade catalítica pela excitação SPR, mostrando que a excitação do SPR também pode levar a efeitos detrimentais sobre a atividade catalítica dependendo do mecanismo de reação estudado e natureza de intermediários na etapa determinante da velocidade de reação. Como as propriedades de nanoestruturas metálicas são fortemente dependentes de tamanho, forma e composição, acreditamos que os resultados apresentados aqui relatados podem ter implicações importantes para o design de nanomateriais unidimensionais com características/propriedades desejadas para aplicações em diversas áreas, incluindo óptica e catalise. / In the first part of this thesis, we focused on the utilization of an approach based on controlled oxidative etching for the removal of seeds/nuclei promoted by the addition of HCl in the polyol synthesis of silver nanowires (Ag). This allowed a precise control over the width of the Ag nanowires in the 65-765 nm range. In this case, the widths showed a linear increase with the HCl concentration employed in the reaction. While the width was also dependent on other experimental parameters such as the concentration of AgNO3 and polyvinylpyrrolidone (PVP) as well as the temperature, oxidative etching promoted by HCl enabled the control over a wider range of sizes. We also investigated the optical properties of Ag nanowires as a function of their size and their applications as substrates for surface enhanced Raman scattering (SERS). In the second part of this work, Ag-Au, Ag-Pt, and Ag-Pd nanotubes displaying controlled surface morphologies were obtained by galvanic replacement reaction between the Ag nanowires and AuCl4-, PtCl62-, e PdCl42- ions, respectively. In this case, while smooth surfaces were obtained at 100 °C, rough surfaces were observed at room temperature. We also showed that smooth surfaces could be obtained by using a saturated solution of NaCl as the solvent during the galvanic reaction. Finally, in the third part of this study, we investigated the effect of surface plasmon resonance (SPR) excitation on Ag nanowires over the catalytic activity towards the 4-nitrophenol reduction. However, our results indicated a drop in catalytic activity with SPR excitation, showing that the SPR excitation can also lead to detrimental effects on the catalytic activity depending on the nature of the chemical reaction mechanism and intermediates in the rate-determining step of the reaction. As properties in metallic nanostructures are strongly dependent on size, shape and composition, we believe that the results reported here may have important implications for the design of one-dimensional nanomaterials design with desired features/properties for applications in various fields that include optics and catalysis.