Raman spectroscopy offers much better spectral selectivity but its usage has been limited by its poor sensitivity. The discovery of surface-enhanced Raman scattering (SERS) effect, which results in increased sensitivities of up to 108-fold for some compounds, has eliminated this drawback. A new SERS active substrate was developed in this study. Silver nanoparticle-doped polyvinyl alcohol (PVA) coated SERS substrate prepared through chemical and electrochemical reduction of silver particles dispersed in the polymer matrix. Performances of the substrates were evaluated with some biologically important compounds. The specific detection of DNA has gained significance in recent years since increasingly DNA sequences of different organisms are being assigned. Such sequence knowledge can be employed for identification of the genes of microorganisms or diseases. In this study, specific proteasome gene sequences were detected both label free spectrophotometric detection and SERS detection. In label free spectrophotometic detection, proteasome gene probe and complementary target gene sequence were attached to the gold nanoparticles separately. Then, the target and probe oligonucleotide-modified gold solutions were mixed for hybridization and the shift in the surface plasmon absorption band of gold nanoparticles were followed. SERS detection of specific nucleic acid sequences are mainly based on hybridization of DNA targets to complementary probe sequences, which are labelled with SERS active dyes. In this study, to show correlation between circulating proteasome levels and disease state we suggest a Raman spectroscopic technique that uses SERGen probes. This novel approach deals with specific detection of elevated or decreased levels of proteasome genes&rsquo / transcription in patients as an alternative to available enzyme activity measurement methods. First, SERGen probes were prepared using SERS active labels and specific proteasome gene sequences. Then DNA targets to complementary SERGen probe sequences were hybridized and SERS active label peak was followed.

The understanding of molecular effects in nanoscale environments is becoming increasingly relevant for various emerging fields. These include spectroscopy for molecular identification as well as in finding molecules for energy harvesting. Theoretical quantum chemistry has been increasingly useful to address these phenomena to yield an understanding of these effects. In the first part of this dissertation, we study the chemical effect of surface-enhanced Raman scattering (SERS). We use quantum chemistry simulations to study the metal-molecule interactions present in these systems. We find that the excitations that provide a chemical enhancement contain a mixed contribution from the metal and the molecule. Moreover, using atomistic studies we propose an additional source of enhancement, where a transition metal dopant surface could provide an additional enhancement. We also develop methods to study the electrostatic effects of molecules in metallic environments. We study the importance of image-charge effects, as well as field-bias to molecules interacting with perfect conductors. The atomistic modeling and the electrostatic approximation enable us to study the effects of the metal interacting with the molecule in a complementary fashion, which provides a better understanding of the complex effects present in SERS. In the second part of this dissertation, we present the Harvard Clean Energy project, a high-throughput approach for a large-scale computational screening and design of organic photovoltaic materials. We create molecular libraries to search for candidates structures and use quantum chemistry, machine learning and cheminformatics methods to characterize these systems and find structure-property relations. The scale of this study requires an equally large computational resource. We rely on distributed volunteer computing to obtain these properties. In the third part of this dissertation we present our work related to the acceleration of electronic structure methods using graphics processing units. This hardware represents a change of paradigm with respect to the typical CPU device architectures. We accelerate the resolution-of-the-identity Moller-Plesset second-order perturbation theory algorithm using graphics cards. We also provide detailed tools to address memory and single-precision issues that these cards often present.

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The effective diagnosis of leukemia subtypes requires the detection of multiple cell surface markers. Current methods of detection use mostly fluorophores, which are limited by their large spectral bandwidths, photobleaching, and incompatibility with histological stains used for morphological assessments. Antibody-conjugated Surface enhanced Raman scattering (SERS) nanoparticles is an alternative tool that overcomes these limitations. A current drawback of SERS is the lack of available tools to analyze the bioconjugation of antibodies to nanoparticles following EDC/sulfo-NHS cross-linking, which produces inconsistent results and determines the efficacy of SERS probe targeting. This study uses the flow cytometry approach to evaluate SERS particles by incorporating FITC and DyLight650 secondary antibodies. Flow cytometry was also used to assess targeting of particles to markers on LY10 cells and CLL cells and to detect SERS signals by inserting a 710 BP 10nm FWHM filter specific for MGITC.

The effective diagnosis of leukemia subtypes requires the detection of multiple cell surface markers. Current methods of detection use mostly fluorophores, which are limited by their large spectral bandwidths, photobleaching, and incompatibility with histological stains used for morphological assessments. Antibody-conjugated Surface enhanced Raman scattering (SERS) nanoparticles is an alternative tool that overcomes these limitations. A current drawback of SERS is the lack of available tools to analyze the bioconjugation of antibodies to nanoparticles following EDC/sulfo-NHS cross-linking, which produces inconsistent results and determines the efficacy of SERS probe targeting. This study uses the flow cytometry approach to evaluate SERS particles by incorporating FITC and DyLight650 secondary antibodies. Flow cytometry was also used to assess targeting of particles to markers on LY10 cells and CLL cells and to detect SERS signals by inserting a 710 BP 10nm FWHM filter specific for MGITC.

This dissertation presents subwavelength optics with focus on the theory and applications of subwavelength apertures in a metal film. Two main issues regarding the optics with subwavelength apertures are investigated. As the first issue, the extraordinary optical transmission (EOT) through a single hole in a metallic waveguide is presented. A total transmission through a single subwavelength aperture is theoretically predicted for a perfect electric conductor regardless of the aperture size, without relying on aperture arrays and surface corrugations as presented in previous works. The waveguide EOT is then applied to boost the optical throughput of an apertured near-field scanning optical microscope (NSOM) probe. Using a new structure for the apertured NSOM probe which allows for waveguide EOT, the optical throughput and the damage threshold are boosted by 100× and 40× as compared to a conventional structure, and the experimental findings are backed-up by comprehensive finite-difference time-domain (FDTD) simulations. Single fluorescent molecules are scanned using the EOT apertured NSOM probe, and a spatial resolution of 62 nm is achieved. As the second issue, subwavelength apertures are found useful for optical trapping. A small dielectric particle can significantly change the optical transmission through an aperture by dielectric loading, and subsequently, a large optical force is induced which favors trapping. A self-induced back-action (SIBA) optical trap is designed using a circular nanohole in a gold film. Trapping of 50 nm polystyrene particle is experimentally achieved, which is not possible using a conventional single beam optical tweezers. The circular nanohole SIBA trap works beyond the perturbative regime, as proven by FDTD simulations and a Maxwell stress tensor analysis. We further improve the nanohole trapping using a double-nanohole, which is more sensitive for small dielectric changes due to the intense local field enhancement between its two sharp tips. A single 12 nm silica sphere is experimentally trapped using the double-nanohole, as the smallest trapped dielectric particle reported. We also achieve the trapping of a single protein – a bovine serum albumin (BSA) protein with a hydrodynamic radius of 3.4 nm in the folded form. The trapped BSA is also unfolded by the large optical force, as confirmed by experiments with changing optical power and changing pH. The high signal-to-noise ratio of 33 in monitoring single protein trapping and unfolding shows a tremendous potential for using the double-nanohole as a sensor for protein binding events at a single molecule level. / Graduate

Many biological processes, pathogens, and pharmaceuticals act upon, cellular membranes. Accordingly, cell membrane mimics are attractive targets for biosensing, with research, pathology, and pharmacology applications. Lipid bilayers represent a versatile sensor functionalization platform providing antifouling properties, and many receptor integration options, uniquely including transmembrane proteins. Bilayer-coated sensors enable the kinetic characterization of membrane/analyte interactions. Addressed theoretically and experimentally is the self-assembly of model membranes on plasmonic sensors. Two categories of plasmonic sensors are studied in two parts. Part I aims to deposit raft-forming bilayers on planar nanoaperture arrays suitable for multiplexing and device integration. By vesicle fusion, planar bilayers are self-assembled on thiol-acid modified flame-annealed gold without the need for specific lipid head-group requirements. Identification of coexisting lipid phases is accomplished by AFM imaging and force spectroscopy mapping. These methods are successfully extended to metallic, plasmon-active nanohole arrays, nanoslit arrays and annular aperture arrays, with coexisting phases observed among the holes. Vis-NIR transmission spectra of the arrays are measured before and after deposition, indicating bilayer detection. Finally, the extraction of membrane proteins from cell cultures and incorporation into model supported bilayers is demonstrated. These natural membrane proteins potentially act as lipid-bound surface receptors. Part II aims to encapsulate in model lipid bilayers, metallic nanoparticles, which are used as probes in surface enhanced Raman spectroscopy. Three strategies of encapsulating particles, and incorporating Raman-active dyes are demonstrated, each using a different dye: malachite green, rhodamine-PE, and Tryptophan. Dye incorporation is verified by SERS and the bilayer is visualized and measured by TEM, with support from DLS and UV-Vis spectroscopy. In both parts, lipid-coated sensors are successfully fabricated and characterized. These results represent important and novel solutions to the functionalization of plasmonic surfaces with biologically relevant cell membrane mimics.

Lithium Ion Batteries (LIBs) are important in today's society, powering cars and mobile devices. LIBs consist of a negative anode commonly made of graphite, and a positive cathode commonly made from transition metal oxides. Between these electrodes are separators and organic solvent based electrolyte. Due to the high potential of LIBs the electrolyte is reduced at the anode. The electrolyte reduction results in the formation of a layer called the Solid Electrolyte Interphase (SEI), which prohibits the further breakdown of the electrolyte. Despite being researched for over50 years, the composition formation of the SEI is still poorly understood. The aim of this project is to develop strategies for efficient identification and classification of various active and intermediate components in the SEI, to, in turn, gain an understanding of the reactions taking place, which will help find routes to stabilize and tailor the composition of the SEI layer for long-term stability and optimal battery performance. For a model gold/li-ion battery electrolyte system, Raman spectra will be obtained using Surface Enhanced Raman Spectroscopy (SERS) in a spectroelectrochemical application where the voltage of the working gold electrode is swept from high to low potentials. Spectra of common components of the SEI as well as similar compounds will be simulated using Density Functional Theory (DFT). The DFT data is also used to calculate the spontaneity of reactions speculated to form the SEI. The simulated data will be validated by comparing it to experimental spectra from pure substances. The spectroelectrochemical SERS results show a clear formation of Li-carbonate at the SERS substrate, as well as the decomposition of the electrolyte into other species, according to the simulated data. It is however shown that there are several issues when modelling spectra, that makes it harder to correlate the simulated spectra with the spectroelectrochemical spectra. These issues include limited knowledge of the structure of the compounds thought to form on the anode surface, and incorrect choices in simulational parameters. To solve these issues, more work is needed in these areas, and the spectroelectrochemical methods used in this thesis needs to be combined with other experimental methods to narrow down the amount of compounds to be modelled. More work is also needed to avoid impurities in the electrolyte. Impurities leads to a thick inorganic layer which prohibits the observation of species in the organic layer.

The presented diploma thesis is focused on finding conditions suitable for the study of surface reactions, especially Suzuki-Miyaura cross-coupling reaction (SMCR), by the surface- enhanced Raman scattering (SERS) method. The first part of the work deals with the optimization of the conditions of individual reactions using the classical synthetic Schlenk technique. Traditional, published, conditions for SMCR were gradually modified during the work so that the reactions could be performed in aqueous media and at room temperature, i.e., under conditions suitable for SERS spectroscopy. The following catalysts were tested: (i) PEPPSI - the traditional SMCR catalyst; (ii) palladium ions; (iii) Pd colloids; (iv) bimetallic colloids of Pd and plasmonic metal (Ag, Au) in the form of core-shell and alloy; (v) Ag and Au colloids with additions of palladium salt or N- heterocyclic carbenes (NHC-catalysts). Two groups of substrates were used: substrates with functional groups with high affinity for the surfaces of metal nanoparticles (NPs) and substrates without these anchoring functional groups. Substrates without the anchoring functional groups can be expected to enter the SMCR reaction from solution. In the second part of this diploma thesis selected reaction mixtures for SMCR were performed in septum...

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