Research toward a multiplexed nucleic acid biosensor that uses quantum dots (QDs) as donors in a fluorescence resonance energy transfer (FRET) assay is described. Optical fibers were modified with mixed films composed of different colours of QDs and different oligonucleotide probes that served as scaffolds for the hybridization of the corresponding target nucleic acid sequences. Fluorescent dyes that were suitable as acceptors for each QD donor were associated with hybridization and provided an analytical signal through FRET-sensitized emission. Different detection channels were achieved through the combination of different donors and acceptors: green emitting QDs with Cyanine 3 or Rhodamine Red-X; and red emitting QDs with Alexa Fluor 647. A detection channel that used the direct excitation of Pacific Blue complemented the FRET pairs. One-plex, two-plex, three-plex and four-plex hybridization assays were demonstrated. A sandwich assay format was adopted to avoid target labeling. Detection limits were 1-10 nM (1-12 pmol) and analysis times were 1-4 h. Single nucleotide polymorphisms were discriminated in multiplexed assays, and the potential for reusability was also demonstrated. Non-selective interactions between QDs and oligonucleotides were characterized, and routes toward the optimization of the QD-FRET hybridization assays were identified. A basic model for multiple FRET pathways in a mixed film was also developed. In addition to the advantages of solid-phase assays, the combination of QDs and FRET was advantageous because it permitted multiplexed detection using a single excitation source and a single substrate, in the ensemble, and via ratiometric signals. Spatial registration or sorting methods, imaging or spatial scanning, and single molecule spectroscopy were not required. The research in this thesis is expected to enable new chip-based biosensors in the future, and is an original contribution to both bioanalytical spectroscopy and the bioanalytical applications of nanomaterials.

The aim of this diploma work is to improve selectivity and sensitivity in DNA-chips by utilizing fluorescence resonance energy transfer (FRET) between conjugated polyelectrolytes (CPEs) and fluorophores. Leclerc and co-workers have presented successful results from studies of super FRET between fluorophore tagged DNA and a CPE during hybridisation of the double strand. Orwar and co-workers have constructed a DNA-chip using standard photo lithography creating a pattern of the hydrophobic photoresist SU-8 and cholesterol tagged DNA (chol-DNA). This diploma work will combine and modify these two ideas to fabricate a improved DNA-chip. Immobilizing of DNA onto surface has been done by using soft lithography. Hydrophobic pattern arises from the poly(dimethylsiloxane) (PDMS) stamp. The hydrophobic pattern will attract chol-DNA that is adsorbed to the chip. Different sets of fluorophores are covalently bound to the DNA and adding CPEs to the complex will make FRET occur between CPE and bound fluorophore. We will here show that the specificity in DNA hybridization by using PDMS patterning was high. FRET clearly occurred, especially with the CPEs as donor to the fluorophore Cy5. The intensity of FRET was higher when the fluorophore and the CPE were conjugated to the same DNA strand. The largest difference in FRET intensity between double stranded and single stranded complexes was observed with the CPE tPOMT. Super FRET has been observed but not yet fully proved. The FRET efficiency was lower with the fluorophore Alexa350 as donor compared to the Cy5/CPE complex. Most of the energy transferred from Alexa350 was extinguished by quenching.

<p>A clinically viable brain-machine interface (BMI) requires a fully-implanted wireless neural acquisition system to limit the impediments of percutaneous connections. For an implanted system with an appreciable telemetry range, and where significant</p><p>neural signal processing is performed continuously, a major obstacle for clinical application is the need for a power source. Existing battery technology and wireless power delivery systems have not addressed the need for a mid-range power supply, capable</p><p>of 1-3 W delivery, that limits both induced noise and temperature rise. These factors are crucial for the succesful operation of a fully-implanted neural acquisition system. This work seeks to fill this void, and presents both a wireless power solution suitable for a neural recording device, and a system capable of real time monitoring of tissue temperature rise.</p><p>During this research, a 2 W transcutaneous energy transfer system (TETS) was designed, built and tested. The TETS was designed specifically for a 96-channel implanted neural data acquisition system, which requires continuous power. The major design constraints were tolerance to coil misalignment, low induced noise,</p><p>and reasonable efficiency. The design of the primary circuit consists of an H-bridge switching network driving a planar spiral Litz wire primary coil. The primary also incoporates a novel circuit for detecting the presence of the secondary. The implanted secondary components include a complimentary planar spiral coil connected to a voltage doubling rectifier. The key approach to mitigating axial coil misalignments was the use of step-down switching regulators in the secondary. With this approach, link efficiency remained nearly constant at 40%, for axial coil displacements of up to 2 cm.</p><p>Noise in the recorded neural signals was minimized using two techniques. First, the 250 kHz operating frequency of the system was tuned, such that the aliased harmonics of the switching frequency lay above the bandwidth of the amplifier used for neural recording. The second approach was to limit the impact of induced displacement currents in the body by physically separating the recording front end from the power supply components. A large titanium enclosure was used to house some of the secondary electronics, and provided a low impedance return path for further</p><p>reduction of current-induced noise.</p><p>Limiting the temperature rise of internal components was also a critical design constraint. The need for real time temperature information led to the design of a six channel temperature measurement system and incorporation of the temperature data into the acquisition system data transmission scheme. This system consisted of bead thermistor temperature transducers, and an off-the-shelf microcontroller with a built-in instrumentation amplifier.</p><p>The TETS and temperature system was fully tested in an ovine model during several acute studies. Recorded temperature rise was limited to approximately 5.5&deg C when the system was implanted at an adequate depth in muscle. The TETS was able to successfully power the 2 W neural acquisition system during a data processing task. Received rectified voltage in the secondary ranged from 14.86 V to 20.2 V, while link efficiency remained virtually constant. Acquired neural data was examined for TETS switching noise. The measured RMS noise increased by less than 1 &mu V, averaged over several experiments. These results demonstrate the first mid-range TETS solution for powering a fully implanted neural acquisition system.</p> / Dissertation

We prove the existence and linear stability of quasi-periodic breather solutions in a 1d Hamiltonian lattice of identical, weakly-coupled, anharmonic oscillators with general on-site potentials and under the effect of long-ranged interaction, via de KAM technique. We prove the persistence of finite-dimensional tori which correspond in the uncoupled limit to N arbitrary lattice sites initially excited. The frequencies of the invariant tori of the perturbed system are only slightly deformed from the frequencies of the unperturbed tori.

Molecular photoabsorption enhancement under ambient solar radiations can improve efficiency substantially in renewable energy production. Here, we explore the theoretical basis and experimental evidences that nanostructured molecular assemblies exhibit an unprecedented property of synergistic photon absorption enhancement. The molecular mechanism of this enhancement phenomenon originates from the combined effect of the photon-molecule interaction and the electronic energy transfer between two adjacent molecular assemblies. For a natural system, the synergistic photon absorption enhancement factor of green algae (Chlorella vulgaris) in vivo at 632.8 nm was determined to be 103. This enhanced photon absorption process in nanostructured molecular assemblies opens a doorway to create entangled double excitons by incoherent solar radiations.

A set of three through-bond energy transfer cassettes based on BODIPY as a donor and cyanine dyes as acceptors has been prepared via Sonogashira couplings, and their photophysical properties were examined. These cassettes fluoresce around 600 to 800 nm and are resolved by approximately 100 nm. This property is an important factor for multiplexing study in cellular imaging. Several useful fluorescent probes such as 5- and 6-carboxyfluorescein, water-soluble BODIPY, and water-soluble Nile Blue dyes, have also been synthesized and their photophysical properties studied. We have also attempted to develop a method for protein mono-labeling via a solidphase approach. The labeling of protein with one fluorescent dye facilitates quantification and single molecule imaging in biological applications. Various solidsupports such as PEGA, CPG, and BSA-coated CPG, were tested. Photolabile and chemically cleavable linkers were prepared to connect solid-supports and fluorophores. Unfortunately, our approach to the fluorescent mono-labeling of native proteins did not give us any conclusive results.

New methodologies for the efficient syntheses of 4,4-difluoro-4-bora-3a,4adiaza- s-indacenes (BODIPYs) and rosamines were developed. A serendipitous discovery led to a new reaction which afforded BODIPYs in high yields. Systematic studies of the kinetics and mechanisms of the new reaction were performed. A series of BODIPYs were successfully prepared using the new approach. A simple and efficient synthesis of rosamines with cyclic-amine substituents was devised. These new rosamines showed interesting anti-tumor activities. Several types of novel fluorescent compounds were prepared. Highly fluorescent GFP-chromophore analogs were designed and synthesized. The correlation between the optical properties and the structures was investigated. New pyronin dyes with mesoheteroatom substituents were efficiently prepared. The fluorescence properties of these compounds were highly dependent on the nature of the meso-substituents. A set of BODIPY dyes that fluoresce brightly above 600 nm were made. They were then used as acceptors to prepare water-soluble through-bond energy transfer cassettes. All the cassettes had complete energy transfer and high quantum yields in MeOH. A few also had good fluorescence properties in aqueous media and even on proteins. The through-bond energy transfer cassettes were used to monitor protein-protein interactions. In order to test our hypothesis, an artificial protein interaction system was built by utilizing the biotin/(strept)avidin interactions. Thus Atto425-BSA-biotin, streptavidin-cassette1 and avidin-cassette2 were prepared. The interactions between Atto425-BSA-biotin and cassette labeled (strept)avidin were successfully detected in vitro and in living cells by fluorescence techniques.

In this thesis, the development and implementation of fluorescence lifetime imaging microscopy that integrates time correlated single photon counting (TCSPC) and a confocal microscope will be described. The TCSPC method has high detection efficiency, with a time resolution limited only by the transit time spread of the detector, and directly delivers the decay functions in the time domain. TCSPC can also be used to obtain images that indicate the fluorescence resonance energy transfer (FRET) effect between critical fluorophores, an important method distinguish the difference between binding and co-localization. Estimation of distances between RET fluorophore pairs can also be established. Additionally, the effects of ion concentration, oxygen concentration, pH value, ..etc. can also be revealed.

An antenna for light harvesting is an organized multicomponent system in which several chromophoric molecular species absorb the incident light and channel the excitation energy to a common acceptor component. In this study, Click chemistry has been successfully applied in the synthesis of a bay region tetraboron dipyrrin (BODIPY) appended perylenediimide (PDI). This light-harvesting molecule presents a large cross section for the absorption of light in the visible region. Excitation energy is efficiently channeled to the perylenediimide core. This novel antenna system is the first demonstration of the efficiency of energy transfer in a BODIPY- PDI bichromophoric system and appears to be highly promising for the design and synthesis of similar dendritic structures.

Energy transfer is a natural phenomena that bases of the photosynthesis. In photosynthesis, chlorophyls and auxlary absorbing dyes units absorb solar energy and transfer the energy to the reaction center where other chemical reactions occur. Studies showed that energy transfer depends strongly on distance and rigidy of the structure. Rigid structures that close in space transfer energy nearly %100 efficiency. Supramolecular chemistry tries to mimic nature and miniurize natural phenomence on to molecular scale. Thus, articifial photosynthesis has been very popular in supramolecular chemistry. A lot of studies have been dedicated to diffent parts of photosynthesis. BODIPY dyes have very well defined photophysical properties that can be used in multichromic systems and designing molecular switching potential tool on in supramolecular chemistry. In this study extended BODIPY dyes constructed on a rigid xanthane scaffold have been deviced for energy transfer.