Nanotechnology builds devices from the bottom up with atomic accuracy. Among the basic nano-components to fabricate such devices, semiconductor nanoparticle quantum dots (QDs), metal nanocrystals, proteins, and nucleic acids have attracted most interests due to their potential in optical, biomedical, and electronic areas. The major objective of this research was to prepare nano-components in order to fabricate functional nano-scale devices. This research consisted of three projects. In the first two projects, we incorporated two desirable characteristics of QDs, which are their abilities to serve as donors in fluorescence energy transfer (FRET) and surface energy transfer (SET) as well as to do multiplexing, to engineer QD-based nanoconjugates for optical and biomedical applications. Immobilizing luminescent semiconductor CdSe/ZnS QDs to a solid platform for QD-based biosensors offers advantages over traditional solution-based assays. In the first project, we designed highly sensitive CdSe/ZnS QD SET-based probes using gold nanoparticles (AuNPs) as FRET acceptors on polystyrene (PS) microsphere surfaces. The emission of PS-QD was significantly quenched and restored when the AuNPs were attached to and then removed from the surface. The probes were sensitive enough to analyze signals from a single bead and for use in optical applications. The new PS-QD-AuNP SET platform opens possibilities to carry out both SET and FRET assays in microparticle-based platforms and in microarrays. In the second project, we applied the QD-encoded microspheres in FRET-based analysis for bio-applications. QDs and Alexa Fluor 660 (A660) fluorophores are used as donors and acceptors respectively via a hairpin single stranded DNA. FRET between QD and A660 on the surface of polystyrene microspheres resulted in quenching of QD luminescence and increased A660 emission. QD emission on polystyrene x microspheres was restored when the targeted complementary DNA hybridized the hairpin strand and displaced A660 away from QDs. The third project involved fabrication of different nanoconjugates via self-assembly of template-based metal nanowires and metal nanoparticles using oligonucleotides as linkers. These nanoconjugates can serve as building blocks in nano-electronic circuits. The template method restricted the oligonucleotides attachment to the tip of the nanowires. Nanowires tagged with hybridizable DNA could connect to complementary DNA-modified metal crystals in a position-specific manner.

Fluorescence energy transfer from poly(9,9-dioctylfluorene) to polymeric energy acceptors that include head-to-tail regioregular poly(3-hexylthiophene or P3HT) and poly(2-methoxy-5(2 -ethylhexyloxy)-1,4-phenylenevinylene) or MEH-PPV and monomeric acceptor meso-tetraphenylporphyrin or TPP was studied and correlated with the underlying morphology when the donor-acceptor blends were prepared as drop-coated films or breath-figure structures. It was found that the phase-separate morphology in films and breath figures was influenced by a number of factors, including material transport dynamics, solubility of the blend components in a solvent, interaction of the solvent with the substrate, and the diffusion rate of the blend components.

[Truncated abstract] Internal waves redistribute energy and momentum in stratified lakes and constitute the path through which the energy that is introduced at the lake scale is cascaded down to the turbulent scales where mixing and dissipation take place. This research, based on intensive field data complemented with numerical simulations, covers several aspects of the energy flux path ranging from basin-scale waves with periods of several hours to high frequency waves with periods of few minutes. It was found that, at the basin-scale level, the horizontal shape of the lake at the level of the metalimnion controls the period and modal structure of the basin-scale natural modes, conforming to the dispersion relationship of internal waves in circular basins. The sloping bottom, in turn, produces local intensification of the wave motion due to focusing of internal wave rays over near-critical slopes, providing hot spots for the degeneration of the basin-scale waves due to shear instabilities, nonlinear processes and dissipation. Different types of high-frequency phenomena were observed in a stratified lake under different forcing conditions. The identification of the generation mechanisms revealed how these waves extract energy from the mean flow and the basin-scale waves. The changes to the stratification show that such waves contribute to mixing in different ways . . . Detailed field observations were used to develop a comprehensive description of an undocumented energy flux mechanism in which shear-instabilities with significant amplitudes away from the generation level are produced in the surface layer due to the shear generated by the wind. The vertical structure of these instabilities is such that the growing wave-related fluctuations strain the density field in the metalimnion triggering secondary instabilities. These instabilities also transport energy vertically to the thermocline where they transfer energy back to the mean flow through interaction with the background shear.

Un-doped, Tb3+ as well as Yb3+ doped ZnO nanocrystals with different concentrations of RE3+ (Tb3+, Yb3+) ions were successfully synthesized via sol-gel method to produce rare earth activated zinc oxide nanophosphors. The phosphor powders were produced by drying the precursor gels at 200˚C in ambient air. Based on the X-ray diffraction results, it was found that the pure and RE3+ doped ZnO nanophosphors were highly polycrystalline in nature regardless of the incorporation of Tb3+ or Yb3+ ions. Moreover, the diffraction patterns were all indexed to the ZnO Hexagonal wurtzite structure and belong to P63mc symmetry group. The Raman spectroscopy confirmed the wurtzitic structure of the prepared samples. Elemental mapping conducted on the as prepared samples using Scanning electron microscope (SEM) equipped with energy dispersive X-ray spectrometer (EDX) revealed homogeneous distribution of Zn, O, and RE3+ ions. The high resolution transmission electron microscope (HR-TEM) analyses indicated that the un-doped and RE3+ doped samples were composed of hexagonal homogeneously dispersed particles of high crystallinity with an average size ranging from 4 to 7 nm in diameter, which was in agreement with X-ray diffraction (XRD) analyses. ZnO:Tb3+ PL study showed that among different Tb3+ concentrations, 0.5 mol% Tb3+ doped ZnO nanoparticles showed clear emission from the dopant originating from the 4f-4f intra-ionic transitions of Tb3+ while the broad defects emission was dominating in the 0.15 and 1 mol% Tb3+doped ZnO. Optical band-gap was extrapolated from the Ultraviolet Visible spectroscopy (UV-Vis) absorption spectra using TAUC‟s method and the widening of the optical band-gap for the doped samples as compared to the un-doped sample was observed. The PL study of ZnO:Yb3+ samples was studied using a 325 nm He-Cd laser line. It was observed that the ZnO exciton peak was enhanced as Yb3+ions were incorporated in ZnO matrix. Furthermore, UV-VIS absorption spectroscopic study revealed the widening of the band-gap in Tb3+ doped ZnO and a narrowing in the case of Yb3+ doped ZnO system. X-ray photoelectron spectroscopy demonstrated that the dopant was present in the doped samples and the result was found to be consistent with PL data from which an energy transfer was evidenced. Energy transfer mechanism was evidenced between RE3+ and ZnO nanocrystals and was discussed in detail. / Physics / M.Sc. (Physics)

Protein-DNA interactions govern the fundamental cellular processes of DNA replication, transcription, repair, and chromosome organisation. Despite their importance, the detailed molecular mechanisms of protein-DNA interactions and their organisation in the cell remain elusive. The complexity of molecular biology demands new experimental concepts that resolve the structural and functional diversity of biomolecules. In this thesis, I describe fluorescence methods that give a direct view on protein-DNA interactions at the single-molecule level. These methods employ photoswitching to control the number of active fluorophores in the sample. Forster Resonance Energy Transfer (FRET) measures the distance between a donor and an acceptor fluorophore to report on biomolecular structure and dynamics in vitro. Because a single distance gives only limited structural information, I developed "switchable FRET" that employs photoswitching to sequentially probe multiple FRET pairs per molecule. Switchable FRET resolved two distances within static and dynamic DNA constructs and protein-DNA complexes. Towards application of switchable FRET, I investigated aspects of the nucleotide selection mechanism of DNA polymerase. I further explored application of single-molecule imaging in the complex environment of the living cell. Photoswitching was used to resolve the precise localisations of individual fluorophores. I constructed a super-resolution fluorescence microscope to image fixed cellular structures and track the movement of individual fluorescent fusion proteins in live bacteria. I applied the method to directly visualise DNA repair processes by DNA polymerase I and ligase, generating a quantitative account of their repair rates, search times, copy numbers, and spatial distribution in the cell. I validated the approach by tracking diffusion of replisome components and their association with the replication fork. Finally, super-resolution microscopy showed dense clusters of SMC (Structural Maintenance of Chromosomes) protein complexes in vivo that have previously been hidden by the limited resolution of conventional microscopy.

Small satellites and CubeSats have established themselves within the aerospace community because of their low cost and high return on investment. Many CubeSats are developed in a short time frame and often leverage commercial off the shelf components for quick turnaround missions. With regard to the Electrical Power System, commercially available products typically use a centralized architecture. However, a centralized architecture is not reusable, since missions that require additional solar arrays or batteries would necessitate a redesign of the power system. With the range of CubeSat sizes and mission goals, it is obvious that a one-size-fits-all solution is not appropriate. This thesis details a reusable and scalable power system architecture applicable to a variety of missions. Reusability is achieved by using common building blocks or "modules," where the same modules can be used between missions. Scalability is achieved by not limiting the number of modules that can be connected together—more modules can be added as needed. In this system, solar arrays and battery units connect directly to a common bus, supplying an unregulated voltage to each subsystem. These subsystems then regulate the bus voltage to their individual needs. The power system also features direct energy transfer and solar-only operation.

Nano-manufacturing is receiving significant attention in industry due to the ever-growing interest in nanotechnology in research institutions. It is hypothesized that single-step or direct-write nano-scale machining might be achieved by coupling nano-probe field emission with radiation transfer. A laser may be used to heat a workpiece within a microscopic region that encloses an even smaller nanoscopic region subjected to a focused electron beam. The electron-beam supplies marginal heat sufficient to remove a minute volume of material by evaporation or sublimation. Experimentally investigating this hypothesis requires an estimate of the power needed in the electron-beam. To this end, a detailed numerical study is conducted to study the possibility of using the nano-probe field emission for nano-machining. The modeling effort in this case is divided into two parts. The first part deals with the electron-beam propagation inside a target workpiece. The second part considers the temperature increase due to the energy transfer between the electron-beam and the workpiece itself. A Monte Carlo/Ray Tracing technique is used in modeling the electron-beam propagation. This approach is identical to that of a typical Monte Carlo simulation in radiative transfer, except that proper electron scattering properties are employed. The temperature distribution inside a gold film is predicted using the heat conduction equations. Details of the various numerical models employed in the simulation and a series of representative results will be presented in this dissertation.

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I have analyzed the interactions between SR proteins and splicing components that are bound at the 5’ or 3’ splice site using fluorescence resonance energy transfer (FRET) microscopy. The SR proteins interact with the U1 snRNP-associated 70 kDa protein (U170K) at the 5’splice site and with the small subunit of the U2 snRNP auxiliary factor (U2AF35) at the 3’ splice site. These interactions have been extensively characterized biochemically in the past, and are proposed to play roles in both intron and exon definition. We employed FRET acceptor photobleaching and fluorescence lifetime imaging microscopy (FLIM) to identify and spatially localise sites of direct interactions of SF2/ASF, and other SR proteins, with U2AF35 and U1-70K in live cell nuclei. These interactions were shown to occur more strongly in interchromatin granule clusters (IGCs). They also occur in the presence of the RNA polymerase II inhibitor, DRB, demonstrating that they are not exclusively co-transcriptional. FLIM data have also revealed a novel interaction between HCC1, a factor highly related to the large subunit of the U2AF splicing factor, with both subunits of U2AF that occur in discrete domains within the nucleoplasm but not within IGCs. These data demonstrate that the interactions defining intron and exon definition do occur in living cells in a transcription-independent manner.