“Lab on a Chip” technologies have revolutionized the field of bio-chemical analytics. The crucial role of optical techniques in this revolution resulted in the emergence of a field by itself, which is popularly termed as “optofluidics”. The miniaturization and integration of the optical parts in the majority of optofluidic devices however still remains a technical challenge. The works described in this thesis focuses on developing integration methods to combine various optical techniques with microfluidics in an alignment-free geometry, which could lead to the development of portable analytical devices, suitable for field applications. The integration approach was applied to implement an alignment-free optofluidic chip for optical chromatography; a passive optical fractionation technique fractionation for cells or colloids. This system was realized by embedding large mode area photonic crystal fiber into a microfluidic chip to achieve on-chip laser beam delivery. Another study on passive sorting envisages an optofluidic device for passive sorting of cells using an optical potential energy landscape, generated using an acousto-optic deflector based optical trapping system. On the analytical side, an optofluidic chip with fiber based microfluidic Raman spectroscopy was realized for bio-chemical analysis. A completely alignment-free optofluidic device was realized for rapid bio-chemical analysis in the first generation by embedding a novel split Raman probe into a microfluidic chip. The second generation development of this approach enabled further miniaturization into true microfluidic dimensions through a technique, termed Waveguide Confined Raman Spectroscopy (WCRS). The abilities of WCRS for online process monitoring in a microreactor and for probing microdroplets were explored. Further enhanced detection sensitivity of WCRS with the implementation of wavelength modulation based fluorescent suppression technique was demonstrated. WCRS based microfluidic devices can be an optofluidic analogue to fiber Raman probes when it comes to bio-chemical analysis. This allows faster chemical analysis with reduced required sample volume, without any special sample preparation stage which was demonstrated by analyzing and classifying various brands of Scotch whiskies using this device. The results from this study also show that, along with Raman spectroscopic information, WCRS picks up the fluorescence information as well, which might enhance the classification efficiency. A novel microfabrication method for fabricating polymer microlensed fibers is also discussed. The microlensed fiber, fabricated with this technique, was combined with a microfluidic gene delivery system to achieve an integrated system for optical transfection with localized gene delivery.

The adsorbate formed by adsorption of thiophenol on a polycrystalline gold electrode and brought into contact with aqueous solutions of 1 M HClO4 and 0.1 M KClO4 has been studied using cyclic voltammetry and surface-enhanced Raman spectroscopy. A strong adsorption is deduced from observations made using cyclic voltammetry. From the SER spectra, interactions of thiophenol with the gold surface via a gold–sulfur bond with the aromatic ring pointing away from the surface is concluded for both electrolyte solutions. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

This thesis reports the investigation of spontaneous Raman Spectroscopy (RS) for its applicability in early drug discovery. A key focus has been to develop an understanding of the applicability of RS for the quantification and localisation of compound concentration inside mammalian cells. Further investigation into the use of Surface Enhanced Raman Spectroscopy (SERS) for research on Visceral Leishmaniasis (VL) and Leishmania donovani as well as investigating applicability for cancer research are decisive parts of this work. The key work described in this thesis is the investigation of whole cell concentration of compounds inside THP-1 and Madin Darby Canine Kidney (MDCK) cells. For true quantification the Cell Silent Region (CSR) is used to measure without interference from cellular background signal. The model compound is erlotinib, an anti-cancer drug with an alkyne group expressing a peak in the CSR. The developed RS system is calibrated using the current gold standard technique Ultra Performance Liquid Chromatography tandem Mass Spectrometry (UPLC-MS/MS). However, because of the single cell nature of the RS information on inter cell variability can be extracted. The RS measurements suggest that there is a large variation of concentration within single cell populations. The RS measurements can therefore give insight in single cell behaviour within a large cell population. Findings shows that washing cycles, before fixation, alter the intra-cellular concentrations significantly. This is hypothesised to be caused by the sudden change in concentration on the outside of the cell that applies an osmotic pressure, leading to loss of substance from inside the cell wall. Localisation of erlotinib is shown within THP-1 cells and points towards an accumulation inside the cell nucleus. Later, internalised Au nano-particles in the range of 30 nm to 80 nm have been investigated for their enhancement effects and localisation inside THP-1 cells. Au nano-particles are found to be internalised easily by differentiated THP-1 cells and accumulate in lysosomes. This allows for a high local enhancement of the spontaneous Raman signal. However, no advantage for the detection of lysosomally trapped compounds (chloroquine, chlorpromazine) was achieved. The detection of substances without a signal in the CSR was achieved without enhancement. Nonetheless, compounds with intrinsic peaks in the CSR could benefit from this enhancement. Lastly the RS system is explored for alternative uses in early drug discovery. This includes the detection of toxicity as well as the discrimination of cell types. Toxicity has been detected using optically trapped THP-1 cells and doxorubicin. Utilising Principal Component Analysis (PCA) combined with Linear Discriminant Analysis (LDA) on these measured spectra, allowed for a clear discrimination of toxically influenced from healthy cells. Differences mainly show up in DNA content caused by the mode of action of doxorubicin and caused by the trapping, which generates most of the signal within the nucleus of the cell. Discriminating cancerogenic (DU145) from healthy prostate cells (PNT2) has been achieved by probing fixed cells and evaluating the acquired Raman spectra with a PCA/LDA combination. The accuracy of separation of these cells when tested with a 10-fold cross-validation technique, is above 98 %, allowing a good discrimination.

The importance of soft matter research, as a major class of materials including liquid crystals, polymers, colloids, emulsions, and forms, is attributed to the behavior resemblances in each branch of soft matter responding to the external perturbations. Hence, one of the most required inquiries in soft matter physics is understanding how the structures with characteristic length scales evolve in response to external perturbations, and concomitant phase transitions. We have focused on adopting polarized Raman spectroscopy to probe phase transitions in soft materials consisting of anisometric components and the evolution of molecular orientational ordering as a complementary tool to other methodologies, but distinct in some respects. The primary task is quantifying the degree of molecular orientation, i.e., obtaining orientational order parameters, in liquid crystal (LCs) system. Thermal evolution of orientation degree in a hitherto elusive biaxial nematic (Nb) phase as well as a commonly known uniaxial nematic (Nu) phase were interrogated from the measurements of anisotropy in polarized Raman intensities. We demonstrated reliable and applicable method to quantify the orientation degree for systems possessing anisotropic ordering. We also addressed a strong potential of Raman spectroscopy that the changes of vibrational energy reflect the variations of intermolecular interactions and structural changes on the molecular level induced by phase transitions. As a subfield of soft matter, we characterized phase transitions and anisotropic ordering observed in an evaporating conjugated polymer solution and elucidated the mechanism of the entities undergoing phase transitions using mainly polarized Raman spectroscopy. In addition, we have shown that tracking Raman spectral changes can provide valuable information for understanding structure-property relations when the measurements of the evolution in physical properties are carried out simultaneously.

The objectives of the work presented were to 1) fabricate reproducible nanorod array SERS substrates, 2) detection of bacteria using nanorod substrates, 3) detection of DNA hybridization using nanorod substrates and 4) critically evaluate the sensing method. Important findings from this work are as follows. A novel method for batch fabrication of substrates for surface enhanced Raman scattering (SERS) has been developed using a modified platen machined to fit in a commercial electron beam evaporator. The use of this holder enables simultaneous deposition of silver nanorod (AgNR) arrays onto six microscope slide substrates utilizing glancing angle deposition. In addition to multiple substrate fabrication, patterning of the AgNR substrates with 36 wells allows for physical isolation of low volume samples. The well-to-well, slide-to-slide, and batch-to-batch variability in both physical characteristics and SERS response of substrates prepared via this method was nominal. A critical issue in the continued development of AgNR substrates is their stability over time, and the potential impact on the SERS response. The thermal stability of the arrays was investigated and changes in surface morphology were evaluated using scanning electron microscopy and x-ray diffraction and correlated with changes in SERS enhancement. The findings suggest that the shelf-life of AgNR arrays is limited by migration of silver on the surface. Continued characterization of the AgNR arrays was carried out using fluorescent polystyrene microspheres of two different sizes. Theory suggests that enhancement between nanorods would be significantly greater than at the tops due to contributing electromagnetic fields from each nanostructure. In contrast to the theory, SERS response of microspheres confined to the tops of the AgNR array was significantly greater than that for beads located within the array. The location of the microspheres was established using optical fluorescence and scanning electron microscopy. The application of SERS to characterizing pathogens such as bacteria and viruses is an active area of investigation. AgNR array-based SERS substrates have enabled detection of pathogens present in biofluids. Specifically, several publications have focused on determining the spectral bands characteristic of bacteria from different species and cell lines. Studies were carried out on three strains of bacteria as well as the medium in which the bacteria were grown. The spectra of the bacteria and medium were surprisingly similar, so additional spectra were acquired for commonly used bacterial growth media. In many instances, these spectra were similar to published spectra purportedly characteristic of specific bacterial species. In addition to bacterial samples, nucleic acid hybridization assays were investigated. Oligonucleotide pairs specifically designed to detect respiratory syncytial virus (RSV) in nasal fluids were prepared and evaluated. SERS spectra acquired on oligos, alone or in combination, contain the known spectral signatures of the nucleosides that comprise the oligo. However, spectra acquired on an oligo with a 5'- or 3' thiol were distinctly different from that acquired on the identical oligo without a thiol pendant group suggesting some control over the orientation of the oligo on the nanorod surface. The signal enhancement in SERS depends markedly upon the location of the probe relative to the substrate surface. By systematic placement of nucleotide markers along the oligo chain, the point at which the nucleotide disappears from the spectrum was identified. The overall findings for AgNR SERS substrates suggest that the applicability of SERS for detecting nucleic acid hybridization is limited. The strong distance dependence coupled with the lack of substrate stability at temperatures required for annealing oligos during hybridization suggest that AgNRs are not the platform to use for hybridization assays.

Moving towards label-free technologies is essential for many clinical and research applications. Raman spectroscopy is a powerful tool in the field of biomedicine for label-free cell characterisation and disease diagnosis, owing to its high chemical specificity. However, Raman scattering is a relatively weak process and can require long acquisition times, thus hampering its integration to clinical technologies. Multimodal analysis is currently pushing the boundaries in biomedicine, obtaining more information than would be possible using a single mode and overcoming any limitations specific to a single technique. Digital holographic microscopy (DHM) is a rapid and label-free quantitative phase imaging modality, providing complementary information to Raman spectroscopy, and is thus an ideal candidate for combination in a multimodal system. Firstly, this thesis explores the use of wavelength modulated Raman spectroscopy (WMRS), for the classification of immune cell subsets. Following this a multimodal approach, combining Raman spectroscopy and DHM, is demonstrated, where each technique is considered individually and in combination. The complementary modalities provide a wealth of information (both chemical and morphological) for cell characterisation, which is a step towards achieving a label-free technology for the identification of human immune cells. The suitability of WMRS to discriminate between closely related neuronal cell types is also explored. Furthermore optical spectroscopic techniques are useful for the analysis of food and beverages. The use of Raman and fluorescence spectroscopy to successfully discriminate between various whisky and extra-virgin olive oil brands is demonstrated, which may aid the detection of counterfeit or adulterated samples. The use of a compact Raman device is utilised, demonstrating the potential for in-field analysis. Finally, monodisperse and highly spherical nanoparticles are synthesised. A short study demonstrates the potential for these nanoparticles to benefit the techniques of surface enhanced Raman spectroscopy and optical trapping, by way of minimising variability.

The polymeric gel-forming mucins provide the structural framework of saliva and the mucus barriers that cover the mucosal surfaces of the alimentary canal. Dietary compounds may influence the barrier properties of these protective layers. The effects of green tea polyphenols, which have many health benefits but have low bioavailability and contribute to the astringency of green tea, on the structural properties of the mucins in the alimentary canal are investigated here. Using well characterised, highly purified salivary mucins MUC5B and MUC7, and porcine gastric mucins, the effects of the green tea polyphenol epigallocatechin-3-gallate (EGCG) on mucins were studied here. Using rate-zonal centrifugation coupled to agarose gel electrophoresis, atomic force microscopy and particle tracking microrheology, EGCG, at concentrations found in a cup of green tea, caused increased aggregation of MUC5B in human whole saliva, and increased aggregation and viscosity of purified MUC5B. It was revealed using recombinant proteins of the N- and C-terminal regions of MUC5B that EGCG had these effects by aggregating the terminal globular protein domains of MUC5B. In contrast, MUC5B trypsin-resistant high molecular weight glycopeptides were not aggregated by EGCG, demonstrating that the oligosaccharide-rich, highly-glycosylated regions of mucins are not involved in the EGCG-induced aggregation of mucins. EGCG also caused the majority of MUC7 in human whole saliva to aggregate, and purified MUC7 also showed substantial aggregation in the presence of EGCG.Porcine gastric mucins were also used in order to model human gastric mucins. First, the identity of the porcine gastric mucins was explored using tandem mass spectrometry and immunohistochemistry. This revealed that Muc5ac was expressed by the surface epithelium and was the prominent mucin in porcine gastric mucus. Muc6 was expressed by gastric submucosal glands, but was not a major component of the secreted mucus barrier. Porcine Muc5ac and Muc6 were shown to be aggregated by EGCG. These data demonstrate that mucins from both saliva and the stomach are substantially altered by EGCG. This may contribute to the astringency and low bioavailability of EGCG. In contrast, the green tea polyphenol epicatechin (EC) did not cause aggregation of salivary mucins or porcine gastric mucins, suggesting that the galloyl ring of EGCG (which is absent in EC) is important for its aggregation of mucins, and that EC has different mechanisms of astringency. The structure of the mucins in the alimentary canal was studied using Raman spectroscopy, Raman optical activity (ROA) and Tip-enhanced Raman spectroscopy (TERS). The secondary structure of the oligosaccharide-rich regions of mucins was shown to be largely disordered, with some contribution of poly-proline II helix. The N- and C-terminal regions of MUC5B were largely β-sheet in structure, with some disordered structure also present in the C-terminal region. Raman spectroscopy could reliably distinguish between MUC5B glycoforms, demonstrating the sensitivity of this technique to mucin glycosylation and secondary structure. The first TERS spectra along the length of a MUC5B chain are reported, and suggest that patterns may exist in the glycosylation of MUC5B. Therefore, Raman spectroscopies are novel tools that shed new light on mucin structure and in future may be useful for studying the changes to mucin structure during interactions, such as those with polyphenols.

[pt] O espaço interplanetário contem partículas de poeira cósmica originárias do meio interestrelar ou que são produtos da erosão de Asteroides, Meteoróides e Cometas. As partículas que chegam à superfície da Terra são chamadas de micro-meteoritos. Os micrometeoritos participam dos processos de erosão da superfície terrestre e, por isso, são estudados para se ter uma melhor compreensão da evolução do nosso planeta e do Sistema Solar. Um novo programa de pesquisa iniciado em 2016 no Departamento de Física da PUC-Rio tem os objetivos de 1) desenvolver um meio experimental para simular os impactos de micrometeoritos com a superfície terrestre e 2) analisar, as mudanças físico-químicas causadas pelos impactos nos minerais terrestres. A fim de simular o impacto dos micrometeoritos, empre-gou-se a técnica de Ablação por Laser, o que permitiu fazer deposições a taxas controladas de energia em áreas determinadas das amostras. Para este trabalho foram escolhidas amostras dos silicatos mais abundantes encontrados na crosta terrestre, como jadeíta, quartzo e feldspato. A ablação dos silicatos foi efetuada em dois meios: amostra no ar ou amostra em H2O. A principal técnica analítica utilizada foi a espectroscopia Raman. Complementarmente foram utilizadas a micros-copia óptica e a perfilometria. Um total de cerca 500 espectros Raman foram obti-dos, e várias bandas para cada amostra nos dois meios, antes e depois da ablação, foram analisadas estatisticamente. A análise energética e morfológica dos impactos por laser mostrou que a técnica de ablação por laser é razoavelmente boa para simular os impactos dos micrometeoritos com a crosta terrestre. A análise dos espetros Raman mostrou que depois da ablação, tanto no ar como em H2O deionizada, os três silicatos apresentaram modificações na intensidade, na largura e na posição do centro de várias das suas bandas principais. Constatou-se que, quando há modificações, o comportamento é o mesmo para todos os silicatos: deslocamento dos centros das bandas para números de onda menores. Os resultados da análise por espectroscopia Raman são encorajantes para a utilização desta técnica na caracterização e interpretação das mudanças espectrais e estruturais na superfície terrestre depois do impacto de micrometeoritos. Este trabalho, no melhor do nosso conheci-mento, nunca foi feito. A perspectiva é dar continuidade a esta linha de pesquisa, aumentando o número de experimentos de ablação por laser e estendendo a análise das amostras irradiadas a outras técnicas de caracterização complementares a espetroscopia Raman (espetroscopia UV-Vis-NIR, FTIR, ....). Além disso, numa fase futura de estudo, serão estudadas amostras mais complexas, onde material orgânico será adicionado aos silicatos já estudados. / [en] The interplanetary space contains particles of cosmic dust that come from the interstellar medium, or that are the product of the erosion of Asteroids, Meteoroids and Comets. The particles that reach the Earth s surface are called micrometeorites. Micrometeorites participate in the erosion processes of the Earth s surface and, therefore, are studied in order to have a better understanding of the evolution of our planet and the Solar System. A new research program was initiated in 2016 in the Department of Physics of PUC-Rio with the objectives of 1) finding an experimental means to simulate the impacts of micrometeorites with the terrestrial surface, and 2) analyzing the physical-chemical changes caused by the impacts on terrestrial minerals. In order to simulate the impact of micrometeorites the Laser Ablation technique was employed, which allowed us to make energy depositions at controlled rates in certain areas of the samples. For this work, we chose samples of the most abundant silicates found in the earth s crust, such as jadeite, quartz and feldspar. The ablation of the silicates was carried out in two medium: the sample in air, and the sample in H2O. The main analytical technique used was Raman spectroscopy. In addition, optical microscopy and profilometry were used. About 500 Raman spectra were obtained, and several bands for each sample and in each medium, before and after ablation, were statistically analyzed. The energetic and morphological analysis of the laser impacts showed that the technique of laser ablation is reasonably good to simulate the impacts of micrometeorites with the terrestrial crust. The analysis of the Raman spectra showed that after the ablation, in air as well as in deionized H2O, all three silicates presented modifications in the intensity, width and position of the center of several of their main bands. It was found that, when there were modifications, the behavior was the same for all silicates: a shift of the center of de bands to smaller wavelengths. The results of the analysis by Raman spectroscopy are encouraging to use this technique in the characterization and interpretation of the spectral and structural changes in the terrestrial surface after the impact of micrometeorites. This work, to the best of our knowledge, has never been done before. Its perspective is to give continuity to this line of research, incrementing the amount of experiments by laser ablation and extending the analysis of the irradiated samples to other characterization techniques that complement Raman spectroscopy (UV-Vis-NIR spectroscopy, FTIR, …). Also, in future studies, more complex samples will be studied, where organic material will be added to the already studied silicates.

No description available.

Increased proliferation of nanotechnology has led to concerns regarding its implication to the water environment. Gold nanoparticles (AuNP) were used as a model nanomaterial to investigate the fate and dynamics of nanoparticles in the complex water environment. A column study was performed to examine the fate and transport of gold nanoparticles with two different coatings in porous media. The resulting data suggested that gold nanoparticles aggregate significantly in the porespace of the column interior, a finding that is not predicted by traditional colloidal filtration theory or Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. Surface-enhanced Raman spectroscopy (SERS) was developed as a new technique to investigate AuNP aggregation in water with varying salt levels. The SERS technique proved valuable as an analytical technique, elucidating information about aggregation as well as AuNP surface interactions with dissolved halides in water. A thorough investigation examining Aunt aggregation with monovalent and divalent salts utilizing SERS, ultraviolet-visible light (UV-Vis) spectroscopy, and dynamic light scattering (DLS) was conducted. Each technique provided data describing different aspects of the dynamic behavior of AuNPs in complex water environments. Results suggest that in addition to attractive and repulsive interactions described by DLVO theory, chemical interactions between the AuNP surface and dissolved halides were also a significant driving force for aggregation and other transformative behaviors of AuNPs in water. The SERS technique developed in this work was shown to be a viable tool to help unveil the vastly complex dynamics of nanomaterial in the water environment. / Ph. D. / Nanotechnology is everywhere. It is in our smartphones, in our food, in our clothes, even if we do not recognize it is there. And this is a good thing, because nanotechnology – that is, technology that utilizes nanomaterials – can provide things that traditional technology often cannot. This is all because many nanomaterials have “superpowers” due to their size range: they are generally larger than what we may think of when we think of chemical molecules, but much smaller than macroscopic materials whose behaviors can be approximated by classic physics and chemistry. For example, we all know that gold has a shiny yellow metallic appearance. However, if we make little particles of gold – and these are going to be very tiny, with diameters about 10,000 times smaller than that of a strand of human hair (but about 100 times larger than what we would typically think of as molecules of chemicals) – and put them in water, the resulting mixture will be ruby-red like wine. One of the “superpowers” these gold nanoparticles possess is that they interact with light in a very different way than bulk gold. Currently, researchers in the biomedical field are producing promising work employing these particles in nextgeneration imaging, and much more. In this study, we were interested in what happens to these materials once they are released to the water environment. Because of the “superpowers” these gold nanoparticles possess, we really do not know how they will behave once they are released to either surface or groundwater because the physics and chemistry of those environments can be quite variable and complex. In this work, we have shown that traditional assumptions about particulate contaminants in water systems do not necessarily hold for gold nanoparticles. Laboratory simulations show that interactions between these particles and the surrounding environment that were once thought to be negligible, are in fact highly significant. As our title suggests, we are developing new and advanced “photonics” methods to help us discover the dynamic complexity dictating the fate of these gold nanoparticles once they are in the water environment. Photonics methods are techniques that employ light as a probing tool. These techniques use a well understood laser light source that is directed towards the particles in a water environment, and we then measure changes in the scattered light after it has interacted with the particles. The technique we have employed here (called surface-enhanced Raman spectroscopy, or SERS) simultaneously provides us information about different behaviors of gold nanoparticles in water, including how they may aggregate (that is, stick to one another and form big clumps) and how they interact with existing dissolved chemicals that may be present in the natural water environment. By pairing this method with other existing methods, we were able to paint a more complete picture of how these nanoparticles behave in the water environment, and we can answer some questions as to why they do not follow some previously held assumptions. In the end, the work in this dissertation will help future scientists continue to unlock the complexity of nanomaterial fate and dynamics in the water environment.