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The technique of Molecular Dynamics (MD) computer simulation is coupled with the interrelated theories of light scattering and atomic polarisability to develop and test models for the Raman scattering from alkali halide systems. The primary interest is in the spectrum and intensity of the scattering from melts, but scattering from crystals is also considered. Two computationally tractable models for the Raman scattering are developed. One, a qualitative model capable of reproducing light scattering lineshapes in Nal, is based on approximations to the quantum-mechanical transition rates for the scattering processes and relies on the shell model interionic potentials from lattice dynamics to give insight into the dynamics of ionic dipole moment fluctuations, from which the scattering behaviour is extracted. The second model is a quantitative one capable of reproducing absolute scattering intensities as well as lineshapes for NaCl melts. This model is based on a detailed parameterisaton of the variation of individual ion polarisabilities with the instantaneous local ionic configuration. The model parameters are extracted from the results of electronic structure calculations on ionic systems performed elsewhere. This model has additionally been applied with some success to NaCl crystal systems. The scattering behaviour of LiF has also been considered, although no experimental comparison is available. The primary failure of the second model is its inability to predict the correct depolarisation ratio for the scattering from NaCl; reasons for this are offered. In developing the models, computer simulation techniques and the light scattering and polarisability theories are reviewed, as are aspects of alkali halide systems, especially interionic potentials suitable for use in simulations. Numerous improvements and extensions to the models are suggested.

Understanding cellular heterogeneity has been a challenge in biology. Current bio-analytical methods such as mass spectrometry or fluorescence-based detection would destruct the sample or perturb the functions of targeted molecules. In situ imaging of bio-molecules at single cell level resolves the phenotypes at metabolomics domain, which can address the challenges in studying cellular heterogeneity. Stimulated Raman scattering (SRS) microscopy provides a label-free approach to identify molecules based on the signature of molecular vibrations. However, there are several challenges to overcome in order to use SRS as a single-cell analysis platform with high throughput, high content, and high sensitivity. My thesis work aims to overcome above-mentioned difficulties. To fulfill the first unmet need of single cell metabolic analysis, we developed an SRS flow cytometry, and demonstrated the discrimination of particles at a throughput of up to 11,000 particles per second, which is a four orders of magnitude improvement compared to conventional spontaneous Raman flow cytometry. Next, we addressed the second unmet need of single-cell metabolic analysis through the development of SRS imaging cytometry. Using this platform, we studied the response of human pancreatic cancer to drug-induced and starvation-induced stress, and discovered lipid-facilitated protrusion as a metabolic biomarker for stress-resistant cancer cells. Lastly, to probe low-concentration bio-molecules using fingerprint Raman bands, we utilized pre-resonance enhancement to increase the SRS signal by two orders of magnitude, and demonstrated ultra-sensitive imaging of retinoids in cells. We demonstrated in situ imaging of retinoid level in cancer cells and during neuronal development. Collectively, these efforts demonstrate SRS cytometry as a high-throughput, high-content, and high-sensitivity single-cell analysis platform with broad applications. / 2022-01-28T00:00:00Z

Surface-enhanced Raman scattering (SERS) has long been the interest of researchers in chemistry, physics and engineering, especially since the discovery that SERS can probe into the system down to the single molecule (SM) level. Despite the large number of publications regarding the fabrication of SERS substrates, it has been a challenge in the field to quantify the SERS signal and universally compare substrates. Traditionally, enhancement factor (EF) is used as an indicator of substrate quality, but the EF calculation is hugely dependent on the estimation of the surface coverage and other factors that are determined largely subjectively. Therefore, this thesis aims at discussing other parameters that can also be used to evaluate different substrates. Six different SERS substrates of Ag or Au nanoparticles of different sizes were fabricated by nanosphere lithography (NSL) and characterized by electron microscopy and UV-vis spectroscopy. SERS substrates were mapped for different concentrations of a probe molecule. Through subsequent baseline correction and principle component analysis (PCA), the "intensity" of individual spectrum was obtained and the shapes of intensity histograms of each substrate were acquired. Instead of calculating EF, five criteria (six quantification methods in total) were employed to comprehensively evaluate the six substrates. These were density of hot spots (characterized by the number of zero-intensity events), enhancement (represented by mean intensity), spatial variation (calculated by RSD of intensity), repeatability (realized by cross correlation) and histogram shape (quantified by skewness and kurtosis). These new methods provide insights to the understanding of the properties of SERS substrates in terms of hot spots. Different substrates may exhibit better performance in terms of one criterion but worse in terms of others. Those variations in performance can be explained by their surface morphology. These more elaborated methods are believed to provide a more comprehensive approach to evaluate and compare substrates than the traditional EF values. The thesis also paves the way for future study on SM-SERS and fabricating better SERS substrates. / Graduate

Amplificadores Ãticos amplificam a luz incidente atravÃs de emissÃo estimulada, o mesmo mecanismo que à usado pelos lasers. Com certeza, um amplificador Ãtico, nÃo à nada mais do que um laser sem realimentaÃÃo. Seu principal ingrediente à o ganho Ãtico que à percebido quando o amplificador à sujeito a um bombeio (oticamente ou eletricamente) para conseguir a inversÃo de populaÃÃo nos subniveis. O ganho Ãtico, em geral, depende nÃo somente da freqÃÃncia (ou comprimento de onda) do sinal incidente, mas tambÃm da intensidade do feixe local em qualquer ponto dentro do amplificador. Esse trabalho foi motivado por uma procura contÃnua do conhecimento e entendimento das caracterÃsticas e dos fenÃmenos envolvidos na amplificaÃÃo de regime de pulso curto que seriam relevantes como aplicaÃÃes para processos nos quais tais fenÃmenos nÃo podem ser negligenciados. Sem perda de generalidade, evitamos sistemas de vÃrios canais, consideramos aqui um Ãnico canal com relaÃÃo a outro, pelo fato de que o ganho e o Ãndice de refraÃÃo ambos dependem do nÃmero de canais envolvidos. Neste trabalho foi simulada inicialmente a amplificaÃÃo Ãptica onde o ganho era constante de modo a comparar com um novo modelo proposto aqui, aonde o ganho à periÃdico. Neste caso modelamos as parcelas de transferÃncia de energia do bombeio e do sinal em funÃÃes periÃdicas de onde foi simulado com diferentes parÃmetros das funÃÃes periÃdicas escolhidas. AlÃm do mais, os efeitos de dispersÃo, automodulaÃÃo de fase, pulso walkoff, efeito Raman e depleÃÃo de pulso foram considerados como fatores importantes para amplificaÃÃo Raman de pulsos curtos. Com relaÃÃo à forma dos pulsos de bombeio e a semente Raman para as simulaÃÃes toma um pulso Gaussiano e um sinal CW fraco respectivamente. O pulso de bombeio transfere energia para o sinal CW ao longo da fibra. Todas as simulaÃÃes foram realizadas usando um mÃtodo numÃrico espectral bem conhecido como Split-Step Fourier Method resolvendo as equaÃÃes acopladas nÃo lineares de SchrÃdinger. / Optical Amplifiers amplify incident light through stimulated emission, the same mechanism which is used by lasers. Indeed, an optical amplifier, it is not but a laser without feedback. Its main ingredient is optical gain which is realized when the amplifier is under pumping process (optically or electrically) in order to cause population inversion at electronic sublevels. In a long run, the optical gain will not only depend on frequency (wavelength) of incident signal, but it also depends on the local beam intensity of the optical gain that is entailed to the amplifier medium. This thesis was stimulated by the continuous pursue of knowledge and understanding of characteristics and phenomena involved in the Raman amplification process in the regime of short pulses which would be relevant as the appliance for processes in which such phenomena can not be neglected. Without loss of generality, we considered the case of where there is an only one channel to another one by the fact that the gain and the refractive index both depend on the number of channels. In this thesis, it has also been simulated the optical amplification where the gain was constant in order to comparing to the periodic gain presented in this thesis. In addition, the effects of dispersion, self phase modulation, pulse walk-off, Raman effects and pulse depletion were considered as important factors for Raman amplification of short pulses. That was also considered for our simulations a weak CW signal or a Raman seed to be amplified by an intense pump Gaussian pulse. All the simulations were achieved using a well-known spectral numerical method namely Split-Step Fourier Method for solving the coupled Nonlinear SchrÃdinger Equations.

Optical transition energies are widely used for providing experimental insight into the electronic band structure of single-wall carbon nanotubes (SWCNTs). While the first and second optical transitions in semiconducting carbon nanotubes have already been heavily studied, due to experimental difficulties in accessing the relevant excitation energy region, little is known about higher lying transitions. Here, I present measurements of the third and fourth optical transitions of small-diameter (0.7-1.2 nm), semiconducting single-wall carbon nanotubes via resonant Raman spectroscopy in the visible deep blue region (415-465 nm) and photoluminescence excitation spectroscopy in the ultraviolet and visible blue optical regions (280-488 nm). Diameter-dependent Raman radial breathing mode features, as well as resonant energy excitation maxima determined by Raman and photoluminescence measurements, are assigned to specific (n,m) nanotube species. The Raman intensity within a given 2n+m branch is found to increase with decreasing chiral angle, consistent with similar measurements for lower order optical states. Additionally, increased excitation line widths and weaker Raman intensities are observed as higher lying transitions are accessed for a given nanotube, in agreement with previous Raman measurements. Chiefly, a scaling law analysis that removes the chiral-angle-dependent contribution to the optical transition energy indicates that the third and fourth transition energies exhibit a significant deviation from the energy trend line observed for the first and second optical transitions, when the transition energies are plotted as a function of nanotube diameter. This deviation can be understood in the context of a change in the competition between exchange and excitonic correction terms. Furthermore, for semiconducting SWCNTs with diameters less than 0.9 nm, an additional deviation is observed that is interpreted as the first observation of crossing-over of the third and fourth transition energy trend lines for a given 2n+m branch and a chirality dependence in the many-body excitonic effects that becomes significant at high nanotube curvatures.

Three investigations were conducted on the nature of the radiance field in clear ocean water. It is important to understand the sunlight intensity below the sea surface because this leads to an understanding of how ocean creatures navigate in shallow and deep water. The nature of the radiance field is also gives an understanding of the living environment for ocean animals. Hydrolight 4.1, a simulation software developed by Curtis D. Mobley, was used to calculate the spectral radiance in clear ocean water for multiple wavelengths from the surface down through the asymptotic region. The first study found, as expected, that Raman scattering has little effect on wavelengths of light that are less than 500 nm. The effect of Raman scattering increases with increasing wavelength, and with increasing depth. The second study found the region of the water column where the radiance field is asymptotic. The third investigation found the effect of changing the mean square slope, or variance of the water-wave slope distribution. This effect is greatest near the surface and for a more truncated mean square slope integral. There are three peaks in percent difference to the ideal case, near the surface, one in the solar beam and the others near the critical angle of water.

Surface enhanced Raman spectroscopy (SERS) has great potential for design of next generation point-of-care (POC) diagnostic devices. However, its practical application in medical diagnosis is limited due to high cost of SERS substrates. The goal for this thesis was to develop affordable SERS substrates, and demonstrate their efficacy in the detection and assay of a Raman probe and diabetes biomarkers, using 514nm and 1064nm Raman spectrometers. Rapid and less energy intensive methods were optimised for manufacturing three categories of SERS substrates: 1) chemically roughened silver (Ag) metal, 2) Ag and gold (Au) nanoparticles (NPs) prepared using microemulsions, and 3) Ag and Au NPs’ coated insoluble electrospun membranes. Immersion of Ag metal for 30 seconds in ammonia (NH4OH), followed by 10 seconds in nitric acid (HNO3) produced optimum roughened Ag metal SERS substrates. For synthesis of gold (Au) and Ag NPs, microemulsion compositions were varied, and the use of sodium borohydrate (NaBH4) produced the desired larger sizes and anisotropic shapes of the NPs. Nanostructured planar SERS structures based on insoluble electrospun membranes, were prepared by covalently binding Au or Ag NPs, on electrospun poly acrylic acid-ethylene glycol (PAA-EG) fibres. Ag metal SERS substrates provided the best SERS enhancement for the Raman probe molecule, 4-methylbenzenethiol (MBT), with a detection limit of 1aM, using 514nm Raman spectrometer. The Ag metal SERS substrates were then used to demonstrate proof-of-concept for the use of SERS for assay of diabetes biomarkers. The higher laser intensity of 106nm Raman caused burning of the dry NPs’ incorporated SERS substrates; but the thermally conductivity of solid Ag in Ag metal SERS substrate allowed SERS detection of 1nM MBT. To conclude, chemically roughened Ag metal SERS substrates proved cost effective and robust for quantitative SERS detection of MBT and diabetes biomarkers both with 514nm and 1064nm Raman spectrometers.

Surface enhanced Raman scattering (SERS) has achieved much attention since its conception in 1974. The analytical technique overcomes many difficulties associated with conventional Raman whilst also increasing sensitivity. However, the increased interest and work in the field has also identified flaws, many of which are centred on the irreproducibility of the SERS enhancement effect. The majority of the work described in this thesis focusses on the ‘optimisation’ of solid-state and solution based SERS systems. Optimisation plays a crucial role in maximising both enhancement effects and reproducibility. Here criteria are outlined for the synthesis of high performance solid-state SERS substrates and the synthesis of a range of substrates is assessed, each with associated pros and cons. The most successful substrate was synthesised by exploiting redox potentials which allow for the direct deposition of silver onto copper foil. The deposition times and temperatures were optimised sequentially to generate a high performance substrate capable of detecting Rhodamine 6G at trace levels. Reproducibility comparisons of the silver on copper (SoC) substrate were carried out against commercial substrates: Klarite and QSERS, multiple univariate and multivariate methods were used to assess the substrates performance. The results confirmed that the SoC substrate performed better than both the commercial substrates. The work also highlights the importance of using multiple data analysis methods in order to assess the performance of a solid-state SERS substrate. Deposition of the silver surface was also successful on British 2p coins allowing the for the detection and discrimination of illegal and legal drugs when coupled with multivariate data analysis methods such as PCA and PLS. Solution based SERS analyses were also carried out successfully using different optimisation strategies. The initial investigation involved careful control of the individual components of a SERS system (nanoparticles, aggregating agents and analyte) in order to establish a low limit of detection for the increasingly abused ‘legal high’ MDAI. The use of a reduced factorial design was then successfully employed to explore a greater number of SERS variables and define a low limit of detection for the class B drug mephedrone. The robust experimental design also allowed an insight into the importance of each of the individual components within a solution based SERS system. The final piece of work carried out was the SERS discrimination of antibiotics: ampicillin, ticarcillin and carbenicillin. Optimisation of the solution based experiment allowed the in-situ hydrolysis of the β-lactam moiety present in ampicillin rendering it pharmacologically inactive to be followed under acidic conditions at concentrations of 10 ppm.