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.

The first part of this thesis examines and compares the separate closure formalisms of Wyld and Martin, Siggia, and Rose (MSR). The simplicity of Wyld’s perturbation scheme is offset by an incorrect renormalisation, this contrasts with the formally exact analysis of MSR. The work here shows that a slight change in Wyld’s renormalisation keeps the main results intact and, in doing so, demonstrates that this formalism is equivalent to MSR. The remainder of the thesis is concerned with turbulent dissipation. A numerical solution of the Local Energy Transfer theory, or LET, is reworked and extended to compute decaying and forced turbulence at large Reynolds numbers. Using this numerical simulation, the phenomenon of turbulent dissipation is investigated. In order to use decaying turbulence to study the turbulent dissipation rate as a function of Reynolds number, it is necessary to choose an appropriate time with which a measurement can be taken. Using phenomenological arguments of the evolution of a turbulent fluid, criteria for establishing such a time are developed. An important study in turbulence is the dissipation rate in the limit of vanishing viscosity, also known as the dissipation anomaly. This thesis derives an equation for the dissipation rate from the spectral energy balance equation. Using the LET computation for both decaying and forced turbulence, results are obtained that can be used along with the equation to study the mechanisms behind the dissipation anomaly. It is found that there is a difference in the behaviour of the normalised dissipation rate between decaying and forced turbulence and, for both cases, it is largely controlled by the energy flux.

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<p>A RET network consists of a network of photo-active molecules called chromophores that can participate in inter-molecular energy transfer called resonance energy transfer (RET). RET networks are used in a variety of applications including cryptographic devices, storage systems, light harvesting complexes, biological sensors, and molecular rulers. In this dissertation, we focus on creating a RET device called closed-diffusive exciton valve (C-DEV) in which the input to output transfer function is controlled by an external energy source, similar to a semiconductor transistor like the MOSFET. Due to their biocompatibility, molecular devices like the C-DEVs can be used to introduce computing power in biological, organic, and aqueous environments such as living cells. Furthermore, the underlying physics in RET devices are stochastic in nature, making them suitable for stochastic computing in which true random distribution generation is critical.</p><p>In order to determine a valid configuration of chromophores for the C-DEV, we developed a systematic process based on user-guided design space pruning techniques and built-in simulation tools. We show that our C-DEV is 15x better than C-DEVs designed using ad hoc methods that rely on limited data from prior experiments. We also show ways in which the C-DEV can be improved further and how different varieties of C-DEVs can be combined to form more complex logic circuits. Moreover, the systematic design process can be used to search for valid chromophore network configurations for a variety of RET applications.</p><p>We also describe a feasibility study for a technique used to control the orientation of chromophores attached to DNA. Being able to control the orientation can expand the design space for RET networks because it provides another parameter to tune their collective behavior. While results showed limited control over orientation, the analysis required the development of a mathematical model that can be used to determine the distribution of dipoles in a given sample of chromophore constructs. The model can be used to evaluate the feasibility of other potential orientation control techniques.</p> / Dissertation

<p>To fully optimize devices for solar energy conversion, a comprehensive understanding of how excitons migrate in materials for solar cell devices is crucial. Understanding the mechanisms behind exciton diffusion and energy transfer will enable the fabrication of highly efficient devices. However to thoroughly study exciton properties, techniques implementing high spatial (nm sizes) and temporal (fs time scales) resolution is required. Herein, we utilize transient absorption microscopy (TAM) with 50 nm spatial resolution and 200 fs temporal resolution to elucidate exciton diffusion in polymeric materials for solar energy conversion.</p> <p>While organic devices are inexpensive and require simpler fabrication procedures than inorganic materials, their device efficiencies often suffer due to their semi-crystalline nature, lending to short diffusion lengths which lead to trap sites and inevitably recombination. It has been demonstrated that achieving long-range exciton diffusion lengths is possible through coherence effects. Coherence can be found in an intermediate electronic coupling region where delocalization and localization compete.</p> <p>To exploit coherence effects, we study polymeric systems in which polymer chains are highly aligned via simple and scalable procedures; semiconducting fibers and solution coated films. In studying the fiber, we first implement polarized photoluminesce (PL) to determine optical ansitropy. From the polarized PL and PL images, it is observed that emission intensities are largest when probing along the transition dipole moment of the polymer. This suggests a type of Förester Resonance Energy Transfer mechanism in which excitons hop from one polymer chain to another.</p> <p>Solution coated polymer films are also studied to understand exciton diffusion as a function of deposition methods. By varying the solution concentration as well as coating rate, we are able to tune the morphology of the film. We observe a strong dependence between diffusion constant and deposition parameters, with diffusion constants of <i>ca.</i> 9, 13 and 33 cm²/s for three different films. The results obtained in this thesis are preliminary steps in an effort to elucidate energy transfer mechanisms and rates.</p><br>

O câncer pode ser definido como um conjunto de mais de 100 doenças causadas pelo crescimento desordenado de células e está entre as cinco doenças que mais causam mortalidade no mundo. Por este motivo, pesquisas tem voltado sua atenção no desenvolvimento de novos fármacos e novos tratamentos que sejam mais eficazes e seletivos para o tratamento e diagnóstico dessas doenças. A terapia fotodinâmica (TFD) tem recebido merecido destaque, pois trata-se de uma terapia não invasiva e seletiva. Esta terapia consiste na ativação de um fotossensibilizador através da irradiação em determinado comprimento de onda da luz visível, que em presença de oxigênio molecular é capaz de produzir oxigênio singleto, desencadeando uma série de reações que culminam na produção de espécies reativas de oxigênio (ERO´s), citotóxicas às células. Portanto, a busca por fotossensibilizadores que sejam eficazes para o uso em TFD torna-se importante. As ftalocianinas são compostos que possuem características químicas que as fazem bons candidatos a fotossensibilizadores, pois possuem forte absorção no visível, são quimicamente estáveis e capazes de produzir oxigênio singleto. Combinar fotossensibilizadores com marcadores fluorescentes é uma estratégica interessante para expandir o uso da TFD, uma vez que desta maneira é possível aliar terapia com diagnóstico por imagem. Neste trabalho, propôs-se o estudo da transferência de energia que ocorre em um sistema combinando ftalocianinas de rutênio e nanopartículas fluorescentes, denominadas pontos quânticos (PQ´s). Foi avaliada também a potencialidade citotóxica de espécies que produzem oxigênio singleto (1O2) em terapia fotodinâmica de neoplasias. Paralelamente realizaram-se ainda os estudos fotoquímicos e fotofísicos, a fim de avaliar o sistema para aplicação em \"teranóstica\". Os resultados demonstraram que os complexos rutênio- ftalocianinas apresentaram características de um bom fotossensibilizador, uma vez que apresentaram citotoxicidade em células de linhagens tumorais após estímulo luminoso em baixas concentrações. Quanto à interação entre ftalocianinas e pontos quânticos, verificou-se que estas demonstraram serem bons supressores de fluorescência das nanopartículas, ocorrendo o mecanismo estático para esta supressão. / Cancer is one of the leading causes of death worldwide. Contemporary therapies do not bring the expected effectiveness and the treatment is often non-selective and its application is associated with several side effects, such as: the possibility of damage to genetic material or induction of secondary cancer process by radiotherapy; increasing resistance of tumor cells to chemotherapeutic agents, which translates into a high social and economic costs; significant reduction in the quality of life of patients underwent surgery and their long and expensive hospitalization. In contrast, antitumor photodynamic therapy (PDT) is a non-invasive method consisting of three components: a chemical compound called photosensitizer, light of a specific wavelength, and oxygen. This combination initiates a series of photochemical reactions leading to generation of reactive oxygen species and/or free radicals, which cause the death of cancer cells. Combining therapy and diagnostics has been the aim of many studies, improving the efficacy of the treatment. In this work, we propose the study of interaction between ruthenium phthalocyanines compounds and CdTe-MPA quantum dot, once in literature is described that quantum dots can transfer energy for phthalocyanines, increasing its citotoxycity. It was evaluated the cytotoxic effects of the species that produced singlet oxygen (1O2) and its effects with different axial ligand in the sctrucuture of ruthenium phthalocyanines complexes. It was performed also photophysics and photochemical studies to evaluate the system for theranotic purposes. The results showed that the ruthenium phthalocyanines are good photosensitizer candidates once it presented high cytotoxity effects against different cancer cells lines after irradiation, even in low concentrations. Regarding to the interaction between phthalocyanines and quantum dots, it was demonstrated that the complexes could quenched the nanoparticles fluorescence occurring the static quenching mechanism.

Au cours de cette thèse, nous avons synthétisé de nouveaux composés en utilisant des macrocycles de porphyrines comme socle pour nos architectures. L'objectif était d'étudier leurs propriétés en optique linéaire et non linéaire. Plus précisément, nous avons synthétisé et caractérisé trois groupes de dendrimères de type fluorényl-porphyrine, une série de porphyrines organométalliques dérivés du ruthénium, et commencé une dernière série de nouvelles porphyrines. Les corrélations entre les propriétés et la structure ont été étudiés, le processus de transfert d'énergie du donneur vers la porphyrine a aussi été évalué. En introduction, nous avons présenté le contexte général de la chimie des porphyrines basé sur quatre aspects: (1) la structure chimique, (2) les voies de synthèse, (3) les propriétés en optique linéaire (4) et en optique non linéaire. Nous avons ensuite présenté les différents travaux qui ont été effectués dans notre groupe, et conclut en proposant de nouvelles structures basées sur ces résultats. Dans le premier chapitre, nous présentons la synthèse d'un groupe de dendrimères dérivés de thiényl-porphyrines. Les unités thiényles font le pont entre les dendrons conjugués de type fluorényle et le coeur de la porphyrine. Le transfert d'énergie pour ces molécules est efficace et ces dernières présentent des propriétés en optique non linéaire qui sont intéressantes avec une amélioration de l'absorption à deux photons (ADP). Dans le deuxième chapitre, nous présentons la synthèse d'une série de composés à base de ruthénium dérivés de la Tétrafluorényl- porphyrine (TFP), pour des applications en optique non linéaire (üNL). Dans le troisième chapitre, nous présentons la synthèse de deux nouveaux dendrons avec des antennes fluorényles terminales greffées en position 9 d'un troisième fluorényle, respectivement par voie conjuguées ou non conjuguées. Puis deux nouveaux dendrimères ont été obtenus par couplage de Sonogashira à partir de ces dendrons sur le coeur porphyrine TFP. Le transfert d'énergie de ces dendrons vers la porphyrine est efficace. Ces molécules présentent des propriétés en optique non linéaire qui sont intéressantes et les résultats en ADP sont très prometteurs. Dans le quatrième chapitre, nous présentons la synthèse de porphyrines avec des bras fluorénones terminales. Ces porphyrines émettent également une luminescence rouge et le transfert d'énergie est très efficace. Comme perspectives, un nouveau type de porphyrine méso-alcynyle est envisagé, pour l' instant nous avons juste synthétisé la génération 0 de cette série de dendrimères: Les quatre bras tluorényles sont pontés au coeur de la porphyrine avec des liens alcynyles, et les études optiques de ces prototypes sont en cours. / During this thesis, we have elaborated new compounds using the porphyrin macrocycle as the basic platform of our architectures. The aim, after their syntheses, was to study the linear optical (LO) and non-linear optical (NLO) properties of these new molecules. More precisely, we have synthesized and characterized three groups of fluorenyl-porphyrin dendrimers, a series of ruthenium organometallic porphyrins, and started a series of new type of porphyrin. Their correlations on optical property-structure have been discussed, as well as the energy transfer processes from the donor fragments to porphyrin core acceptor. In the introduction, we presented the general background of the porphyrin chemistry based on four aspects: ( I) structure, (2) synthetic methods, (3) LO properties and (4) NLO properties. We further reviewed prior porphyrin studies done in our group and proposed new molecular designs based on these results. In the first chapter, we synthesized a group of thienyl porphyrin cored dendrimers. The thienyl units connect the conjugated fluorenyl dendrons to porphyrin ring by alkynyl bridges. The energy transfer (ET) of these porphyrins is very efficient and they present interesting NLO properties with enhanced Two-photon absorption (TPA). In the second chapter, we synthesized a series of ruthenium compounds based on Tetra-fluorenyl porphyrin core (TFP) for NLO applications. In the third chapter, we synthesized two new dendrons with two terminal fluorenyl antennae fi xed on the 9 position of the fluorenyl units in conjugated or non-conjugated way respecti vely. Then two new porphyrin dendrimers were obtained by Sonogashira coupling reaction of these dendrons on TFP porphyrin core. Their ET from dendrons to porphyrin core is very efficient. They present interesting LO properties and the TPA results are very promising. In the fourth chapter, we synthesized a group of TFP cored porphyrins with terminal fluorenone anns. These porphyrins emit red luminescence and the ET is very efficient from the linear arms toward their cores. As perspective, a new type of meso-alkynyl porphyrin series is considered, for the moment we synthesized only the generation 0 of the dendrimers: the four fluorenyl arms of this porphyrin are bridged to the centre ring by alkynyl chains, and the optical studies of this prototype are in progress.