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Metabolic activity is an important functional parameter of a living cell. Microscopic techniques are demanded to resolve the heterogeneity of metabolic activity from cell to cell and among subcellular compartments. Towards this, work in the Min lab has been dedicated to developing a prevailing metabolic imaging platform that couples chemical imaging by stimulated Raman scattering (SRS) microscopy with small vibrational tags on precursor molecules. This thesis describes efforts along metabolic imaging by SRS microscopy, with focus on visualizing protein and lipid homeostasis. Chapter 1 describes the design principle of metabolic imaging, including selection of vibrational tags and setup of SRS microscopy, and an overview of successful demonstrations of metabolic imaging in protein and lipid metabolism. Chapter 2 describes adoption of such principle to visualize protein turnover with 13C-phenylalanine metabolic labeling under steady-state condition and various perturbations. The rest of this thesis (Chapters 3-6) switches focus to fatty acid metabolism and cellular lipid homeostasis. As the minimal tagging in vibrational imaging preserves the physicochemical property of lipid molecules to the largest extent, it motivated me to revisit fatty acid metabolism from a biophysical perspective. Bearing the question in mind whether the non-equilibrium metabolic activity could drive phase separation in biological membranes, I thus look into the principle of membrane organization and its implication in biological membranes in Chapter 3. Then in Chapter 4, I describe the discovery and characterization of previously unknown phase separation in endoplasmic reticulum (ER) membrane caused by lipid synthesis. In this case, metabolic imaging by SRS enables identification of solid-like domains formed by saturated fatty acid (SFA) metabolites. This observation further raises the question whether phase separation bears any functional roles in the adverse effects of SFAs (or lipotoxicity). Towards this, Chapter 5 introduces the background of lipotoxicity including its definition and models. Then I review proposed mechanisms for lipotoxicity, which point to the central role of ER in mediating the stress transduction. In Chapter 6, I present our findings that suggest the association of the observed solid-like domains with ER structural remodeling and local autophagic arrest. Together, these efforts demonstrate the valuable capability of SRS imaging to reveal metabolic heterogeneity and how this aids in the investigation of metabolic stress.

No presente trabalho estudou-se os processos de interação entre uma série de porfirinas catiônicas e a melanina. Utilizou-se as porfirinas (Zn-(tetra(4-N-Metilpiridil)porfina): (\'ZN\'-(tetra(4-\'N\'-Metilpiridil)porfina): \'ZN\'-\'T\'\'M\'\'PY\'\'P\', (\'ZN\'-(tetra(4-\'N\'-Benzilpiridil)porfina): \'ZN\'-\'T\'\'BZ\'\'PY\'\'P\', as respectivas porfirinas de base livre (\'T\'\'M\'\'PY\'\'P\' e \'T\'\'BZ\'\'PY\'\'P\') e a melanina sintética obtida a partir da auto-oxidação da dihidroxifenilalanina (L-DOPA). O trabalho baseou-se em três técnicas espectroscópicas complementares: espectroscopia eletrônica (absorção na região do ultravioleta-visível), fluorescência e espalhamento Raman ressonante. Demonstrou-se a formação de complexos estáveis como resultado da interação porfirina-melanina. A partir dos dados de espectroscopia Raman fez-se uma atribuição de bandas vibracionais para as porfirinas, comparando-se com os dados disponíveis na literatura para porfirinas semelhantes. Discutiu-se as possíveis mudanças de estruturas provocadas pela melanina na porfirina, baseadas nas diferenças entre os espectros Raman das porfirinas puras e dos complexos porfirina-melanina. Sugeriu-se uma nova interpretação para os espectros eletrônicos das porfirinas baseada no modelo de Gouterman (modelo de quatro orbitais). A partir dessa interpretação do espectro eletrônico analisou-se a perturbação causada pela melanina nos orbitais moleculares da porfirina fazendo=se uma discussão dos espectros de emissão fluorescente das mesmas. Estimou-se a taxa de transferência de energia da porfirina para melanina através da supressão da fluorescência da porfirina, usando-se medidas de fluorescência com resolução temporal. Demonstrou-se que a fluorescência do complexo porfirina-melanina tem um tempo de vida menor que 5 ps. Utilizou-se as medidas de supressão de fluorescência em regime estacionário para determinar as constantes de dissociação do complexo porfirina-melanina e os possíveis sítios de ligação da melanina. Os resultados evidenciam a importante propriedade do polímero de melanina em atuar como eficiente meio para a dissipação não radiativa de estados eletrônicos excitados. / In this work we studied the interaction between some cationic porphyrins and melanin. The porphyrins used were (\'ZN\'-(tetra(4-\'N\'-Metilpiridil)porfina): \'ZN\'-\'T\'\'M\'\'PY\'\'P\', (\'ZN\'-(tetra(4-\'N\'-Benzilpiridil)porfina): \'ZN\'-\'T\'\'BZ\'\'PY\'\'P\', and their respective free bases porphyrins (\'T\'\'M\'\'PY\'\'P\' e \'T\'\'BZ\'\'PY\'\'P\'). Synthetic melanin was obtained from the auto-oxidation of the 3,4-dihydroxyphenylalanine (L-DOPA). From resonance Raman spectra an attribution is made to the vibrational bands of the porphirins, analyzing the effects of the substituents. The possible changes in the porphyrin structure due to the interaction with melanin are discussed based on the modifications of the resonance Raman spectra of the porphyrins in the presence of melanin. From optical absorption and fluorescence measurements it is suggested a new interpretation to the eletronic spectra of the porphyrins based on the Goutermans model. The perturbation due to the melanin in the molecular orbitals of the porphyrins is also analysed. An estimation of the energy transfer rate to the melanin by time resolved fluorescence measurements of the porphyrin-melanin solution is made. It is demonstrated that the fluorescence lifetime of the porphyrin-melanin complexes are lesser than 5ps. The dissociation constants of the porphyrin-melanin complexes and possible sites of binding of the melanin are determined by fluorescence quenching of the porphyrins as observed by steady state measurements. The results show clearly the important role of the melanin to act as an efficient way to the non-radiative dissipation of the excited electronic states of the porphyrins.

No presente trabalho estudou-se os processos de interação entre uma série de porfirinas catiônicas e a melanina. Utilizou-se as porfirinas (Zn-(tetra(4-N-Metilpiridil)porfina): (\'ZN\'-(tetra(4-\'N\'-Metilpiridil)porfina): \'ZN\'-\'T\'\'M\'\'PY\'\'P\', (\'ZN\'-(tetra(4-\'N\'-Benzilpiridil)porfina): \'ZN\'-\'T\'\'BZ\'\'PY\'\'P\', as respectivas porfirinas de base livre (\'T\'\'M\'\'PY\'\'P\' e \'T\'\'BZ\'\'PY\'\'P\') e a melanina sintética obtida a partir da auto-oxidação da dihidroxifenilalanina (L-DOPA). O trabalho baseou-se em três técnicas espectroscópicas complementares: espectroscopia eletrônica (absorção na região do ultravioleta-visível), fluorescência e espalhamento Raman ressonante. Demonstrou-se a formação de complexos estáveis como resultado da interação porfirina-melanina. A partir dos dados de espectroscopia Raman fez-se uma atribuição de bandas vibracionais para as porfirinas, comparando-se com os dados disponíveis na literatura para porfirinas semelhantes. Discutiu-se as possíveis mudanças de estruturas provocadas pela melanina na porfirina, baseadas nas diferenças entre os espectros Raman das porfirinas puras e dos complexos porfirina-melanina. Sugeriu-se uma nova interpretação para os espectros eletrônicos das porfirinas baseada no modelo de Gouterman (modelo de quatro orbitais). A partir dessa interpretação do espectro eletrônico analisou-se a perturbação causada pela melanina nos orbitais moleculares da porfirina fazendo=se uma discussão dos espectros de emissão fluorescente das mesmas. Estimou-se a taxa de transferência de energia da porfirina para melanina através da supressão da fluorescência da porfirina, usando-se medidas de fluorescência com resolução temporal. Demonstrou-se que a fluorescência do complexo porfirina-melanina tem um tempo de vida menor que 5 ps. Utilizou-se as medidas de supressão de fluorescência em regime estacionário para determinar as constantes de dissociação do complexo porfirina-melanina e os possíveis sítios de ligação da melanina. Os resultados evidenciam a importante propriedade do polímero de melanina em atuar como eficiente meio para a dissipação não radiativa de estados eletrônicos excitados. / In this work we studied the interaction between some cationic porphyrins and melanin. The porphyrins used were (\'ZN\'-(tetra(4-\'N\'-Metilpiridil)porfina): \'ZN\'-\'T\'\'M\'\'PY\'\'P\', (\'ZN\'-(tetra(4-\'N\'-Benzilpiridil)porfina): \'ZN\'-\'T\'\'BZ\'\'PY\'\'P\', and their respective free bases porphyrins (\'T\'\'M\'\'PY\'\'P\' e \'T\'\'BZ\'\'PY\'\'P\'). Synthetic melanin was obtained from the auto-oxidation of the 3,4-dihydroxyphenylalanine (L-DOPA). From resonance Raman spectra an attribution is made to the vibrational bands of the porphirins, analyzing the effects of the substituents. The possible changes in the porphyrin structure due to the interaction with melanin are discussed based on the modifications of the resonance Raman spectra of the porphyrins in the presence of melanin. From optical absorption and fluorescence measurements it is suggested a new interpretation to the eletronic spectra of the porphyrins based on the Goutermans model. The perturbation due to the melanin in the molecular orbitals of the porphyrins is also analysed. An estimation of the energy transfer rate to the melanin by time resolved fluorescence measurements of the porphyrin-melanin solution is made. It is demonstrated that the fluorescence lifetime of the porphyrin-melanin complexes are lesser than 5ps. The dissociation constants of the porphyrin-melanin complexes and possible sites of binding of the melanin are determined by fluorescence quenching of the porphyrins as observed by steady state measurements. The results show clearly the important role of the melanin to act as an efficient way to the non-radiative dissipation of the excited electronic states of the porphyrins.

Cobalt-substituted carboxypeptidase and carbonic anhydrase were chosen as candidates for resonance Raman spectroscopy because they possess visible absorption due to the Co(II)-protein complex. However, no evidence for resonance-enhanced peaks due to the cobalt-containing chromophore was found with laser excitation near the visible absorption bands (514.5 nm) or closer to the ultraviolet absorption bands (457.9nm). Arsanilazocarboxypeptidase and model azotyrosine compounds were selected for a Raman spectroscopic investigation because they have intense absorption bands in the visible region. All of these substances yielded similar resonance Raman spectra. Although there was no evidence for specific zinc-ligand vibrations, shifts in vibrational frequencies of the azotyrosine chromophore could be used as proof of zinc complexation. The protonated azotyrosine model compound was found to have the phenoxy group hydrogen bonded to the azo group, forming a six-membered ring. Replacement of the proton by zinc resulted in the zinc atom being bound only to the phenoxy group. In arsanilazocarboxypeptidase the azotyrosine at position 248 in the polypeptide chain was found to have a structure similar to the protonated model compound, a six-membered ring with zinc bridging the phenoxy group and the azo group. This gave further proof that Tyr 248 is close to the zinc atom in the native enzyme, even in the absence of substrate.

Carbon nanotubes and graphene have been a trending research topic in the past decade. These graphitic compounds exhibit numerous advantageous properties (electronic, mechanical, thermal, optical, etc) which industry and researchers alike are excited to take advantage of. Beyond the challenges of yield and controlled growth, there are a number of standing questions which govern some of the more fundamental characteristics of these materials: What role do lattice defects play in the adsorption of gas molecules on the surface of carbon nanotubes? How are the electronic states of the carbon nanotubes influenced by these adsorbed molecules? And how can we develop models to predict useful applications of this knowledge? In order to address these questions, this study combines Raman spectroscopy and electronic measurements carried out in highly controlled environments of carbon nanotube transistors. Assessing these data in conjunction shows that the defect density of a carbon nanotube channel has no correlation with observed threshold voltage shifts, or change in Schottky barrier, due to the presence of ambient oxygen. With these insights in mind, a dynamic adsorption-desorption model is proposed which addresses the oxygen sensitivity of carbon nanotube transistors. Instrumentation and computational developments which facilitated these measurements are also disclosed.

This thesis reports the spectroscopic and computational studies of a number of Cu(I), Re(I) and Ru(II) complexes of polypyridyl ligands. The ligands considered in this study were 1,10-phenanthroline, 4,7-diphenyl-1,10-phenanthroline, 3,4,7,8-tetramethyl-1,10-phenanthroline, dibenzo[b,j][1,10]phenanthroline, dipyrido[2,3-a:3�,2�-c]phenazine, dipyrido[2,3-a:3�,2�-c]-6,7-dichlorophenazine and dipyrido[2,3-a:3�,2�-c]-6,7-dimethylphenazine. Density functional theory calculations were carried out on the polypyridyl ligands. Validation of the calculations was carried out by comparison of the predicted values to observables. The structures were compared to previously published X-ray crystal data. Calculated bond lengths were typically calculated to be within 0.02 Å of those in the crystal structure. The calculated vibrational spectra were compared to measured IR and Raman spectra. The correspondence between calculated and measured frequencies was quantified using the mean absolute deviation between the two sets of frequencies. This was typically found to be less than 10 cm⁻�. The robustness of the calculation was further tested by calculations on perdeuterated analogues of some of the ligands. The calculations were extended to metal moieties and validated as for the ligands. Resonance Raman and infrared spectra of the reduced states of some Re(I) complexes are reported. The structure and spectra have been modelled by considering the radical anion of the polypyridyl ligand and the reduced state of the complex. There is improvement in the mean absolute deviation, between calculated and observed frequencies, upon incorporation of the metal moiety into the calculation. Spectra are successfully modelled confirming the validity of the modelled structures. The resonance Raman and infrared spectra of the metal-to-ligand charge transfer excited states of some Cu(I), Re(I) and Ru(II) complexes are reported. Density functional theory calculations on the lowest energy triplet states aided in the spectral assignment of bands. Cu(I) complexes were successfully modelled with mean absolute deviations, between calculated and observed frequencies, of less than 10 cm⁻�. The spectra of the Re(I) and Ru(II) complexes were less successfully modelled. Incorporation of the Ru(II) centre into the calculation of the vibrational frequencies of dipyrido[2,3-a:3�,2�-c]phenazine complexes offers no improvement over modelling the radical anion of this polypyridyl ligand. The excited state lifetimes of a number of polypyridyl complexes have been reported. The changes in lifetimes of similar complexes were found to be consistent with the energy gap law or changes in the conjugation of the involved polypyridyl ligand. This project has allowed the excited state structures of a number of polypyridyl complexes to be determined using vibrational spectroscopy to validate density functional theory calculations. This has provided a study strategy that may be applied to other metal polypyridyl complexes.

Graduation date: 1998

Graduation date: 1994

Wurtzite GaN epilayers grown by metal organic chemical vapor deposition on sapphire substrates were subsequently ion implanted with Er to a dose of 5×10¹⁵ cm⁻². The implanted samples were annealed in nitrogen atmosphere at different temperatures to facilitate recovery from implantation related damage. In this paper we report the annealing behavior of Erbium implanted GaN by using micro Raman spectroscopy and optimized annealing condition. We have observed almost full damage recovery of the crystalline quality of Er implanted GaN after annealing at 1000°C for 2 minute. This observation is further confirmed by using AFM images. / Singapore-MIT Alliance (SMA)