A novel type of white light emitting semiconductor quantum dot was characterized at the ensemble and single-molecule level. This kind of semiconductor nanocrystal can be made into white light emitting diodes, which have the potential to replace conventional lighting sources. The quantum dots used in this thesis consisted of a cadmium selenide (CdSe) core, capped with ZnS, and have a surface polymer coating of poly(acrylic acid) (PAA). We have characterized the quantum dot size distribution by using dynamic light scattering (DLS), transmission electron microscopy (TEM), atomic force microscopy (AFM) and UV-Vis spectroscopy. Based on these measurements, it is clear that the white quantum dots are polydisperse, with a core size of 2.4 ± 0.5 nm, though the polymer coating swells considerably in aqueous solution. In order to explore the optical properties, the absorption and emission spectra of the ensemble quantum dots solution were measured and compared to “standard” commercial quantum dots. The emission spectrum of the white quantum dots showed two peaks, a strong blue emission peak and a weaker red emission peak. The fluorescence quantum yield of the white quantum dots was found to be less than that of commercial quantum dots. To explore the behavior of individual quantum dots, spatially-resolved single-molecule images were obtained by a dual-view single molecule fluorescence microscopy with a beam splitter which can separate the emission into red and blue components. It was found that individual white CdSe nanocrystals have a broad emission spectrum and the samples did not consist of a mixed population of red emitters and blue emitters. These results suggest that these white light emitting quantum dots can be used for pure white light LEDs and are a good candidate for the replacement for conventional lighting sources.

Single-molecule fluorescence spectroscopy techniques such as Fluorescence Correlation Spectroscopy (FCS) and single-molecule Förster Resonance Energy Transfer (smFRET) not only possess an unprecedented high sensitivity but also have high temporal and spatial resolution. Therefore, they have an immense potential both in investigation of fundamental biological principles and in clinical applications. FCS analyses are based on both theoretical approximations of the beam geometry and assumptions of the underlying molecular processes. To address the accuracy of analysis, firstly the experimental conditions that should be fulfilled in order to obtain reliable physical parameters are discussed and the input parameters are carefully controlled accordingly to demonstrate the performance of FCS measurements on our home-built confocal multiparameter photon-counting microscope in several in vitro and in-vivo applications. Secondly, we performed a comprehensive FCS analysis of rhodamine family of dyes to evaluate the validity of assigning the correlation relaxation times to the time constant of conformational dynamics of biomolecules. While it is the common approach in literature our data suggests that conformational dynamics mainly appear in the correlation curve via modulation of the dark states of the fluorophores. The size and shape of the folded, unfolded and chemically-denatured states of the N-terminal Src-homology-3 of downstream of receptor kinases (DrkN SH3) were investigated by FCS and smFRET burst experiments. Based on the data, we conclude that a considerable sub-population of the denatured protein is in a closed loop state which is most likely formed by cooperative hydrogen bonds, salt bridges and nonpolar contacts. As a clinical application, we developed and characterized an ultrasensitive capillary electrophoresis method on our multiparameter confocal microscope. This allowed us to perform Direct Quantitative Analysis of Multiple microRNAs (DQAMmiR) with about 500 times better sensivity than a commercial instrument. Quite remarkably, we were able to analyze samples of cell lysate down to the contents of a single cell.

Single-molecule fluorescence spectroscopy techniques such as Fluorescence Correlation Spectroscopy (FCS) and single-molecule Förster Resonance Energy Transfer (smFRET) not only possess an unprecedented high sensitivity but also have high temporal and spatial resolution. Therefore, they have an immense potential both in investigation of fundamental biological principles and in clinical applications. FCS analyses are based on both theoretical approximations of the beam geometry and assumptions of the underlying molecular processes. To address the accuracy of analysis, firstly the experimental conditions that should be fulfilled in order to obtain reliable physical parameters are discussed and the input parameters are carefully controlled accordingly to demonstrate the performance of FCS measurements on our home-built confocal multiparameter photon-counting microscope in several in vitro and in-vivo applications. Secondly, we performed a comprehensive FCS analysis of rhodamine family of dyes to evaluate the validity of assigning the correlation relaxation times to the time constant of conformational dynamics of biomolecules. While it is the common approach in literature our data suggests that conformational dynamics mainly appear in the correlation curve via modulation of the dark states of the fluorophores. The size and shape of the folded, unfolded and chemically-denatured states of the N-terminal Src-homology-3 of downstream of receptor kinases (DrkN SH3) were investigated by FCS and smFRET burst experiments. Based on the data, we conclude that a considerable sub-population of the denatured protein is in a closed loop state which is most likely formed by cooperative hydrogen bonds, salt bridges and nonpolar contacts. As a clinical application, we developed and characterized an ultrasensitive capillary electrophoresis method on our multiparameter confocal microscope. This allowed us to perform Direct Quantitative Analysis of Multiple microRNAs (DQAMmiR) with about 500 times better sensivity than a commercial instrument. Quite remarkably, we were able to analyze samples of cell lysate down to the contents of a single cell.

In the cancer research, it is important to understand protein dynamics which are involved in cell signaling. Therefore, particular protein detection and analysis of target protein behavior are indispensable for current basic cancer research. However, it usually performed by conventional biochemical approaches, which require long process time and a large amount of samples. We have been developed the new applications based on microfluidics and Raster image Correlation spectroscopy (RICS) techniques. A simple microfluidic 3D hydrodynamic flow focusing device has been developed for quantitative determinations of target protein concentrations. The analyte stream was pinched not only horizontally, but also vertically by two sheath streams by introducing step depth cross junction structure. As a result, a triangular cross-sectional flow profile was formed and the laser was focused on the top of the triangular shaped analyte stream. Through this approach, the target protein concentration was successfully determined in cell lysate samples. The RICS technique has been applied to characterize the dynamics of protein 53 (p53) in living cells before and after the treatment with DNA damaging agents. P53 tagged with Green Fluores-cent Protein (GFP) were incubated with and without DNA damaging agents, cisplatin or eptoposide. Then, the diffusion coefficient of GFP-p53 was determined by RICS and it was significantly reduced after the drug treatment while that of the one without drug treatment was not. It is suggested that the drugs induced the interaction of p53 with either other proteins or DNA. This result demonstrates that RICS is able to detect protein-protein or protein-DNA interactions in living cells and it may be useful for the drug screening. As another application of microfluidics, an integrated microfluidic platform was developed for generating collagen microspheres with encapsulation of viable cells. The platform integrated four automated functions on a microfluidic chip, (1) collagen solution cooling system, (2) cell-in-collagen microdroplet generation, (3) collagen microdroplet polymerization, and (4) incubation and extraction of the microspheres. This platform provided a high throughput and easy way to generate uniform dimensions of collagen microspheres encapsulating viable cells that were able to proliferate for more than 1 week.

No description available.

The emergence of unique or enhanced physical, chemical and optical material properties at the nanoscale underlies the swift rise of nanomaterials science over recent decades. Within this interdisciplinary field, catalysis performed by nanomaterials (i.e. nanocatalysis) is one area where differences between nanoscale and bulk material properties offer particularly attractive opportunities for application. The consequent pursuit of viable nanomaterials with unprecedented catalytic activity has inevitably expanded across the periodic table, whereby a number of highly efficient precious metal, metal oxide and composite nanostructured catalysts have been developed for a wide range of synthetic organic and inorganic transformations. The lanthanide series has not been excluded from this search, but is still underrepresented in catalysis despite some rich chemistry and reactivity which sets these elements apart from many other metals. More recently however, the necessary paradigm shift away from commonly utilized but expensive, potentially toxic precious metal catalysts, and toward more sustainable alternatives, has seen an upsurge in the development of novel nanomaterials for heterogeneous catalysis: the general topic of this doctoral thesis. Heterogeneous nanocatalysis offers distinct advantages over homogeneous catalysis. Catalyst recyclability, ease of separation from reaction mixtures, and minimal product contamination all contribute to the higher overall effectiveness of heterogeneous catalysts relative to their homogeneous counterparts. The use of light as an abundant reagent, both in nanomaterial fabrication and for photocatalysis, is another attractive prospect. This dissertation addresses both points, describing the iterative development and application of photochemically-prepared samarium oxide based nanomaterials for heterogeneous catalysis and photocatalysis. Through a series of related peer-reviewed publications and associated commentary, the evolution of the application-driven design of a nanomaterial which is both efficient and effective for a diversity of heterogeneous catalytic and photocatalytic transformations is presented. Major findings include 1) both colloidal and supported samarium oxide nanoparticles can be prepared photochemically and comprise primarily Sm2O3 but may contain localized mixed valences or dynamic surface oxidation states; 2) colloidal samarium oxide nanoparticles possess high activity for Brønsted acid and oxidative catalysis, but recyclability and overall effectiveness is less than optimal due to a combination of polydispersity and size-dependent catalytic activity; 3) a similarly-prepared “second generation” samarium oxide/titanium dioxide nanocomposite presented several advantages over its predecessor, performing highly efficient and effective pure heterogeneous, dual photoredox-Lewis acid catalysis in two different types of synthetically relevant photocyclizations. Effects of different nanoparticle supports, rare insights into the catalytic mechanisms and behaviour of these nanomaterials‒obtained at the single molecule level by innovative application of Total Internal Reflection Fluorescence Microscopy (TIRFM) to catalysis research‒as well as advances in TIRFM data analysis protocols, are also discussed.

abstract: This thesis describes several approaches to next generation DNA sequencing via tunneling current method based on a Scanning Tunneling Microscope system. In chapters 5 and 6, preliminary results have shown that DNA bases could be identified by their characteristic tunneling signals. Measurements taken in aqueous buffered solution showed that single base resolution could be achieved with economic setups. In chapter 7, it is illustrated that some ongoing measurements are indicating the sequence readout by making linear scan on a piece of short DNA oligomer. However, to overcome the difficulties of controlling DNA especially ssDNA movement, it is much better to have the tunneling measurement incorporated onto a robust nanopore device to realize sequential reading of the DNA sequence while it is being translocated. / Dissertation/Thesis / Ph.D. Physics 2011

The aggregation of alpha-synuclein (αS) protein from soluble monomer into solid amyloid fibrils in the brain is associated with a range of devastating neurodegenerative disorders such as Parkinson’s disease. Soluble oligomers formed during the aggregation process are highly neurotoxic and are thought to play a key role in the onset and spreading of disease. Despite their importance, these species are difficult to study by conventional experimental approaches owing to their transient nature, heterogeneity, low abundance and a remarkable sensitivity of the oligomerisation process to the chosen experimental conditions. In this thesis, well-established single-molecule techniques have been utilised to study the aggregation and oligomerisation of αS in solution.

abstract: Fluorescence spectroscopy is a powerful tool for biophysical studies due to its high sensitivity and broad availability. It is possible to detect fluorescence from single molecules allowing researchers to see the behavior of subpopulations whose presence is obscured by “bulk” collection methods. The fluorescent probes used in these experiments are affected by the solution and macromolecular environments they are in. A misunderstanding of a probe’s photophysics can lead researchers to assign observed behavior to biomolecules, when in fact the probe is responsible. On the other hand, a probe’s photophysical behavior is a signature of the environment surrounding it; it can be exploited to learn about the biomolecule(s) under study. A thorough examination of a probe’s photophysics is critical to data interpretation in both cases and is the focus of this work. This dissertation investigates the photophysical behavior of symmetric and asymmetric cyanines in a variety of solution and biomolecular environments. Using fluorescent techniques—such as time-correlated single photon counting (TCSPC) and fluorescence correlation spectroscopy (FCS)—it was found that cyanines are influenced by the local environment. In the first project, the symmetric cyanines are found to be susceptible to paramagnetic species, such as manganese(II), that enhance the intersystem crossing (ISC) rate increasing triplet blinking and accelerating photobleaching. Another project found the increase in fluorescence of Cy3 in the protein induced fluorescence enhancement (PIFE) technique is due to reduced photoisomerization caused by the proximity of protein to Cy3. The third project focused on asymmetric cyanines; their photophysical behavior has not been previously characterized. Dy630 as a free dye behaves like Cy3; it has a short lifetime and can deactivate via photoisomerization. Preliminary experiments on Dy dyes conjugated to DNA show these dyes do not photoisomerize, and do not show PIFE potential. Further research will explore other conjugation strategies, with the goal of optimizing conditions in which Dy630 can be used as the red-absorbing analogue of Cy3 for PIFE applications. In summary, this dissertation focused on photophysical investigations, the understanding of which forms the backbone of rigorous fluorescent studies and is vital to the development of the fluorescence field. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2017

abstract: Single molecule DNA Sequencing technology has been a hot research topic in the recent decades because it holds the promise to sequence a human genome in a fast and affordable way, which will eventually make personalized medicine possible. Single molecule differentiation and DNA translocation control are the two main challenges in all single molecule DNA sequencing methods. In this thesis, I will first introduce DNA sequencing technology development and its application, and then explain the performance and limitation of prior art in detail. Following that, I will show a single molecule DNA base differentiation result obtained in recognition tunneling experiments. Furthermore, I will explain the assembly of a nanofluidic platform for single strand DNA translocation, which holds the promised to be integrated into a single molecule DNA sequencing instrument for DNA translocation control. Taken together, my dissertation research demonstrated the potential of using recognition tunneling techniques to serve as a general readout system for single molecule DNA sequencing application. / Dissertation/Thesis / Ph.D. Biochemistry 2013