Na primeira parte desta dissertação, nos concentramos na utilização de uma abordagem baseada na remoção oxidativa controlada de sementes/núcleos promovida pela adição de HCl na síntese poliol de nanofios de prata (Ag). Isto possibilitou um controle fino sobre a espessura dos nanofios gerados na faixa de de 65 a 765 nm, no qual as larguras obtidos apresentaram um aumento linear em função do aumento na concentração de HCl utilizado na reacção. Embora a largura também se mostrou dependente de outros parâmetros experimentais, tais como a concentração de AgNO3 e polivinilpirrolidona (PVP) e temperatura, remoção oxidativa promovida por HCl possibilitou o controle sobre uma faixa de tamanhos mais ampla. Também investigamos as propriedades ópticas dos nanofios de Ag em função do seu tamanho e sua aplicabilidade como substratos para detecção atraves do fenômeno de espalhamento Raman intensificado por superfície (SERS). Na segunda parte deste trabalho, nanotubos de Ag-Au, Ag-Pt e Ag-Pd contendo morfologias de superfície controladas foram obtidos através da reação de substituicão galvânica entre os nanofios de Ag e íons AuCl4-, PtCl62-, e PdCl42-, respectivamente. Nesse caso, superfícies lisas foram obtidas a 100 oC enquanto superfícies rugosas foram observadas a temperatura ambiente. Mostramos ainda que superfícies lisas também puderam ser obtidas usando-se uma solução saturada de NaCl como solvente durante a reação galvânica. Na terceira parte deste trabalho, investigamos o efeito da excitação da ressonância plasmônica de superfície (SPR) nos nanofios de Ag sobre a atividade catalítica frente a redução do 4-nitrofenol. Contudo, nossos resultados mostraram um queda da atividade catalítica pela excitação SPR, mostrando que a excitação do SPR também pode levar a efeitos detrimentais sobre a atividade catalítica dependendo do mecanismo de reação estudado e natureza de intermediários na etapa determinante da velocidade de reação. Como as propriedades de nanoestruturas metálicas são fortemente dependentes de tamanho, forma e composição, acreditamos que os resultados apresentados aqui relatados podem ter implicações importantes para o design de nanomateriais unidimensionais com características/propriedades desejadas para aplicações em diversas áreas, incluindo óptica e catalise. / In the first part of this thesis, we focused on the utilization of an approach based on controlled oxidative etching for the removal of seeds/nuclei promoted by the addition of HCl in the polyol synthesis of silver nanowires (Ag). This allowed a precise control over the width of the Ag nanowires in the 65-765 nm range. In this case, the widths showed a linear increase with the HCl concentration employed in the reaction. While the width was also dependent on other experimental parameters such as the concentration of AgNO3 and polyvinylpyrrolidone (PVP) as well as the temperature, oxidative etching promoted by HCl enabled the control over a wider range of sizes. We also investigated the optical properties of Ag nanowires as a function of their size and their applications as substrates for surface enhanced Raman scattering (SERS). In the second part of this work, Ag-Au, Ag-Pt, and Ag-Pd nanotubes displaying controlled surface morphologies were obtained by galvanic replacement reaction between the Ag nanowires and AuCl4-, PtCl62-, e PdCl42- ions, respectively. In this case, while smooth surfaces were obtained at 100 °C, rough surfaces were observed at room temperature. We also showed that smooth surfaces could be obtained by using a saturated solution of NaCl as the solvent during the galvanic reaction. Finally, in the third part of this study, we investigated the effect of surface plasmon resonance (SPR) excitation on Ag nanowires over the catalytic activity towards the 4-nitrophenol reduction. However, our results indicated a drop in catalytic activity with SPR excitation, showing that the SPR excitation can also lead to detrimental effects on the catalytic activity depending on the nature of the chemical reaction mechanism and intermediates in the rate-determining step of the reaction. As properties in metallic nanostructures are strongly dependent on size, shape and composition, we believe that the results reported here may have important implications for the design of one-dimensional nanomaterials design with desired features/properties for applications in various fields that include optics and catalysis.

Surface plasmons are collective oscillations of free electrons excited at a metal-dielectric interface by incident light. They possess a broad set of interesting properties including a high degree of tunability, the generation of strong field enhancements close to the metal's surface and high sensitivity to their adjacent dielectric environment. It is possible to enhance the sensitivity of plasmonic systems by using narrow plasmon resonances. In this thesis two approaches to narrowing surface plasmon resonances have been studied: diffraction coupling of localised surface plasmon resonances in gold nanoarrays and the use of graphene-protected copper thin films. Applications of these approaches in hybrid systems have been considered for modulation, waveguiding, biosensing and field enhancements. Arrays of gold nanostripes fabricated on a gold sublayer have been used to create extremely narrow plasmon resonances using diffraction coupling of localised plasmon resonances with quality factors up to a value of $Q \sim 300$, among the highest reported in the literature. The nanostructures were designed to give the narrowest resonance at the telecommunication wavelength of 1.5 µm, allowing for this array geometry to be used in hybrid systems for proof-of-concept optoelectronic devices. The gold nanostripe array was used in a hybrid nanomechanical electro-optical modulator along with hexagonal boron nitride (hBN) and graphene. The modulator was fabricated with an air gap between the nanoarray and the hexagonal boron nitride/graphene. Applying a gate voltage across the device moves the hBN towards the nanoarray, resulting in broadband modulation effects from the ultraviolet through to the mid-infrared dependant on the motion of the hBN instead of graphene gating. The deposition of a 400 nm hafnium(IV) oxide film on top of the gold nanoarray created a structure capable of guiding modes at 1.5 µm. The hybrid air-dielectric-stripe waveguide is capable of guiding modes over a distance of 250 µm. Copper thin films have stronger plasmon resonances and higher phase sensitivity than gold thin films. Transferring a graphene sheet on the copper prevents oxidation of the copper. A feasibility study of this hybrid system has shown that phase-sensitive graphene-protected copper biosensing can detect HT-2 mycotoxin with over four orders of magnitude greater sensitivity than commercially-available gold-based surface plasmon resonance biosensing systems. In summary, two methods of attaining narrow plasmon resonances have been demonstrated and their promise in modulation, waveguiding and biosensing have been demonstrated.

Optical detection devices such as optical biosensors and optical spectrometers are widely used in many applications for the functions of measurements, inspections and analysis. Due to the large dimension of prisms and gratings, the traditional optical devices normally occupy a large space with complicated components. Since cheaper and smaller optical devices are always in demand, miniaturization has been kept going for years. Thanks to recent fabrication advances, nanophotonic devices such as semiconductor laser chips have been growing in number and diversity. However, the optical biosensor chips and the optical spectrometer chips are seldom reported in the literature. For the reason of improving system integration, the study of ultra-compact, low-cost, high-performance and easy-alignment optical biosensors and optical spectrometers are imperative. This thesis is an endeavor in these two subjects and will present our research work on studying the optical transmission properties of dielectric aperture arrays and developing new optical biosensors and optical spectrometers. / Subsequently, optical transmission properties through a self-mixing interferometer array are studied and a novel high-resolution cost-effective optical spectrometer is proposed. The miniature interferometer-based spectrometer is made of polymethyl methacrylate (PMMA) with a CCD as the detector. The detected intensity of each CCD pixels contains the spectral information. Since each frequency component in the incoming beam corresponds to a unique phase difference of the two beam portions of each optical interferometer, the total intensity received by each CCD pixel, which is resulted from the addition of the interference signals from all the frequency components in the beam, should also be unique. Therefore, the spectrum calculation is a problem to solve an ill-posed linear system by using Tikhonov regularization method. Simulation results show that the resolution can reach picometer level. Apart from the choice of path difference between the interfering beams, the spectral resolution also depends on the signal-to-noise ratio and analogue-digital conversion resolution (dynamic range) of the CCD chip. In addition, the theory of uniform waveguide scattering is explored to expand the possibility of using such mini-interferometers for performing free-space spectral analysis of waveguide devices. At the same time, the method of least squares is used to correct the pixel non-uniformity of the CCD so as to improve the performance of the spectrometer. / The first half of the thesis demonstrates that the optical phase shift associated with the surface plasmon (SP) assisted extraordinary optical transmission (EOT) in nano-hole arrays fabricated in a metal film has a strong dependence on the material refractive index value in close proximity to the holes. A novel refractive index sensor based on detecting the EOT phase shift is proposed by building a model. This device readily provides a 2-D biosensor array platform for non-labeled real-time detection of a variety of organic and biological molecules in a sensor chip format, which leads to a high packing density, minimal analyte volumes, and a large number of parallel channels while facilitating high resolution imaging and supporting a large space-bandwidth product (SBP). Simulation (FDTD Solutions, Lumerical Solutions Inc) results indicate an achievable sensitivity limit of 4.37x10-9 refractive index units (RIU) and a dynamic range as large as 0.17 RIU. / The sensor chip and spectrometer chip introduced here are based on the interference of light transmitted through dielectric aperture arrays. Their compact feature renders these devices ideal for miniaturization and integration as the systems in microfluidics architectures and lab-on-chip designs. / Yang, Tao. / Adviser: H. P. Ho. / Source: Dissertation Abstracts International, Volume: 72-04, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 150-163). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

This dissertation comprises experimental studies on the synthesis and applications of metallic nanoshells. These are a class of nanoparticles composed of a dielectric core and a thin metallic shell. Metallic nanoshells play an important role in nanotechnology, particularly in nanomedicine, due to their peculiar optical properties. The overall objectives of the dissertation were to improve the fabrication of these nanoparticles, and to demonstrate new applications of these materials in cancer research and spectroscopy. The fabrication of nanoshells is a multi-step process. Previously to our work, the procedures for the synthesis of nanoshells reported in the literature lacked systematic characterization of the various steps. The procedure was extremely time-consuming and the results demonstrated a high degree of size variation. In Chapter 3, we have developed characterization tools that provide checkpoints for each step of the synthesis. We demonstrated that it is possible to control the degree of coverage on the shell for a fixed amount of reagents, and also showed important differences on the shell growth phase for gold and silver. The synthetic optimization presented in Chapter 3 led to an overall faster protocol than those previously reported. Although the improvements presented in Chapter 3 led to a higher degree of control on the synthesis of nanoshells, the variations in the resulting particle population were still too large for applications in single particle spectroscopy and imaging. In Chapter 4, the synthesis was completely reformulated, aiming to narrow the size distribution of the nanoshell colloids. Through the use of a reverse microemulsion, we were able to fabricate ultramonodisperse silica (SiO2) cores, which translate into nanoshell colloids with narrow extinction bands that are comparable to those of a single nanoshell. We then fabricate a library of colloids with different core sizes, shell thicknesses and composition (gold or silver). The localized surface plasmon resonance (LSPR) of these colloids span across the visible range. From this library, two nanoshells (18nm silver on a 50nm SiO2 core, and 18nm gold on a 72nm SiO2 core) were selected for a proof of principle cell imaging experiment. The silver nanoshells were coated with a nuclear localization signal, allowing it to target the nuclear membrane. The gold nanoshells were coated with an antibody that binds to a receptor on the plasma membrane of MCF-7 human breast cancer cells. The nanoshells were easily distinguishable by eye in a dark field microscope and successful targeting was demonstrated by hyperspectral dark field microscopy. A comparison was made between fluorescent phalloidin and nanoshells, showing the superior photostability of the nanoparticles for long-term cell imaging. The results from Chapter 4 suggest that the nanoshells obtained by our new synthetic route present acceptable particle-to-particle variations in their optical properties that enables single particle extinction spectroscopy for cell imaging. In Chapter 5 we explored the use of these nanoshells for single-particle Surface-enhanced Raman spectroscopy (SERS). Notice that particle-to-particle variations in SERS are expected to be more significant than in extinction spectroscopy. This is because particle-to-particle SERS variabilities are driven by subtle changes in geometric parameters (particle size, shape, roughness). Two types of gold nanoshells were prepared and different excitation wavelengths (λex) were evaluated, respective to the LSPR of the nanoshells. Individual scattering spectra were acquired for each particle, for a total of 163 nanoshells, at two laser excitation wavelengths (632.8 nm and 785 nm). The particle-to-particle variations in SERS intensity were evaluated and correlated to the efficiency of the scattering at the LSPR peak. Chapter 6 finally shows the application of gold nanoshells as a platform for the direct visualization of circulating tumor cells (CTCs). 4T1 breast cancer cells were transduced with a non-native target protein (Thy1.1) and an anti-Thy1.1 antibody was conjugated to gold nanoshells. The use of a transduced target creates the ideal scenario for the assessment of nonspecific binding. On the in vitro phase of the study, non-transduced cells were used as a negative control. In this phase, parameters such as incubation times and nanoshell concentration were established. A murine model was then developed with the transduced 4T1 cells for the ex vivo portion of the work. Non-transduced cells were implanted in a control group. Blood was drawn from mice in both groups over the course of 29 days. Antibody-conjugated nanoshells were incubated with the blood samples and detection of single CTCs was achieved in a dark field microscope. Low levels of nonspecific binding were observed in the control group for non-transduced cells and across different cell types normally found in peripheral blood (e.g. lymphocytes). All positive and negative subjects were successfully identified. Chapter 7 provides an outlook of the work presented here and elaborates on possible directions to further develop the use of nanoshells in bioapplications and spectroscopy. / Graduate / 2019-05-03

abstract: Proteins play a central role to human body and biological activities. As powerful tools for protein detections, many surface plasmon resonance based techniques have been developed to enhance the sensitivity. However, sensitivity is not the only final goal. As a biosensor, four things really matter: sensitivity, specificity, resolution (temporal/spatial) and throughput. This dissertation presents several works on developing novel plasmonic based techniques for protein detections on the last two aspects to extend the application field. A fast electrochemically controlled plasmonic detection technique is first developed with the capability of monitoring electrochemical signal with nanosecond response time. The study reveals that the conformational gating of electron transfer in a redox protein (cytochrome c) takes place over a broad range of time scales (sub-µs to ms). The second platform integrates ultra-low volume piezoelectric liquid dispensing and plasmonic imaging detection to monitor different protein binding processes simultaneously with low sample cost. Experiment demonstrates the system can observe binding kinetics in 10×10 microarray of 6 nL droplet, with variations of kinetic rate constants among spots less than ±5%. A focused plasmonic imaging system with bi-cell algorithm is also proposed for spatial resolution enhancement. The two operation modes, scanning mode and focus mode, can be applied for different purposes. Measurement of bacterial aggregation demonstrates the higher spatial resolution. Detections of polystyrene beads binding and 50 nm gold nanoparticles oscillation show a high signal to noise ratio of the system. The real properties of protein rely on its dynamic personalities. The above works shed light upon fast and high throughput detection of protein kinetics, and enable more applications for plasmonic imaging techniques. It is anticipated that such methods will help to invoke a new surge to unveil the mysteries of biological activities and chemical process. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2018

Luk, Wai Chun = / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 101-108). / Abstracts in English and Chinese. / Luk, Wai Chun = / Chapter 1 --- Introduction --- p.1 / Chapter 2 --- Theoretical Background --- p.5 / Chapter 2.1 --- Maxwell´ةs equations in matter --- p.5 / Chapter 2.2 --- Dielectric constant of materials --- p.8 / Chapter 2.3 --- Dispersion relation of surface plasmon polaritons --- p.10 / Chapter 2.4 --- Excitation of surface plasmon polaritons --- p.16 / Chapter 2.4.1 --- Prism coupling --- p.17 / Chapter 2.4.2 --- Grating coupling --- p.21 / Chapter 2.5 --- Diffraction of light in gratings --- p.26 / Chapter 2.6 --- Applications --- p.27 / Chapter 3 --- Analysis Methods --- p.29 / Experimental Section --- p.29 / Chapter 3.1 --- Interference Lithography --- p.29 / Chapter 3.2 --- Gold grating fabrication --- p.32 / Chapter 3.2.1 --- Substrate preparation --- p.33 / Chapter 3.2.2 --- Photoresist preparation --- p.34 / Chapter 3.2.3 --- Spin coating of omnicoat and photoresist --- p.35 / Chapter 3.2.4 --- Interference lithography set-up and procedures --- p.35 / Chapter 3.2.5 --- The post-exposed treatments --- p.37 / Chapter 3.2.6 --- The optimal exposure time calibration --- p.37 / Chapter 3.2.7 --- Gold thin film deposition --- p.39 / Chapter 3.2.8 --- Typical gold grating sample --- p.41 / Chapter 3.3 --- Measurement system --- p.41 / Chapter 3.3.1 --- The angle dependent reflectivity measurement --- p.42 / Chapter 3.3.2 --- Data presentation of a typical band structure --- p.45 / Chapter 3.3.3 --- Periodicity measurement of the grating samples --- p.48 / Chapter 3.3.4 --- Diffracted intensity measurement of gratings --- p.52 / Chapter 3.3.5 --- Data presentation of the angle dependent diffracted intensity measurement --- p.53 / Calculation Section --- p.54 / Chapter 3.4 --- RCWA simulations --- p.54 / Chapter 3.4.1 --- The dispersion relation --- p.56 / Chapter 3.4.2 --- The diffracted intensity --- p.56 / Chapter 3.4.3 --- The field pattern graphs --- p.57 / Chapter 4 --- Resonance modes in one-dimensional gold gratings --- p.60 / Chapter 4.1 --- Structure of the gold grating samples --- p.61 / Chapter 4.2 --- Results of angle dependent reflectivity --- p.63 / Chapter 4.2.1 --- Surface Plasmon Polaritons (SPPs) --- p.65 / Chapter 4.2.2 --- Wood´ةs anomaly --- p.65 / Chapter 4.2.3 --- Waveguide Resonance (WG) --- p.67 / Chapter 4.2.4 --- Coupling of SPPs and WG --- p.67 / Chapter 4.3 --- Results of angle dependent diffracted intensity measurement --- p.68 / Chapter 4.4 --- Basic properties of SPPs and WG modes by RCWA --- p.73 / Chapter 4.4.1 --- Sample 1 (D = 40 nm) --- p.74 / Chapter 4.4.1(a) --- λ = 980 nm of Sample 1 --- p.75 / Chapter 4.4.1(b) --- λ = 633 nm of Sample 1 --- p.81 / Chapter 4.4.2 --- Sample 2 (D = 390 nm) --- p.83 / Chapter 4.4.2(a) --- λ = 980 nm of Sample 2 --- p.85 / Chapter 4.4.2(b) --- λ = 725 nm of Sample 2 --- p.87 / Chapter 4.4.2(c) --- λ = 633 nm of Sample 2 --- p.92 / Chapter 4.5 --- Summary --- p.97 / Chapter 5 --- Conclusions --- p.99 / Bibliography --- p.101

Sham, Chun Hong = 金屬光栅光學特性的實驗和理論研究 / 沈鎮康. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 109-111). / Abstract also in Chinese. / Sham, Chun Hong = Jin shu guang shan guang xue te xing de shi yan he li lun yan jiu / Shen Zhenkang. / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Background --- p.1 / Chapter 1.2 --- Overview of the Thesis --- p.2 / Chapter 2 --- Basic Theory --- p.4 / Chapter 2.1 --- Dielectric Constant of Metals --- p.5 / Chapter 2.2 --- The Maxwell´ةs Equations --- p.7 / Chapter 2.3 --- Scaling Properties of the Maxwell´ةs Equations --- p.9 / Chapter 2.4 --- Translational Symmetry and the Bloch´ةs Theorem --- p.10 / Chapter 2.4.1 --- Continuous Translational Symmetry --- p.11 / Chapter 2.4.2 --- Discrete Translational Symmetry --- p.12 / Chapter 2.4.3 --- Photonic Bloch´ةs Theorem --- p.13 / Chapter 3 --- Principles of Rigorous Coupled Wave Analysis --- p.14 / Chapter 3.1 --- Mathematical Formulation --- p.15 / Chapter 3.2 --- One-layer systems --- p.15 / Chapter 3.3 --- Layered Systems --- p.19 / Chapter 3.3.1 --- Matching Boundary Conditions --- p.19 / Chapter 3.3.2 --- The Transfer Matrices --- p.21 / Chapter 3.3.3 --- Scattering Matrices --- p.22 / Chapter 3.4 --- Calculation of Reflection and Transmission --- p.24 / Chapter 3.5 --- Calculation of Field Pattern --- p.26 / Chapter 3.5.1 --- Finding the Coefficients --- p.26 / Chapter 3.5.2 --- Summing to Get the Field --- p.27 / Chapter 3.6 --- 5-polarization --- p.27 / Chapter 3.7 --- Analogy to mechanics --- p.29 / Chapter 3.8 --- Conclusion --- p.30 / Chapter 4 --- Numerical Implementation of Rigorous Coupled Wave Analysis --- p.31 / Chapter 4.1 --- Finite Number of Terms --- p.31 / Chapter 4.2 --- Fourier Factorization Rule --- p.32 / Chapter 4.3 --- Calculation of Field Pattern --- p.34 / Chapter 4.4 --- Transfer Matrix for Forward Deduction --- p.36 / Chapter 4.5 --- Calculation of Time-Averaged Poynting Vector --- p.36 / Chapter 4.6 --- Convergence of RCWA --- p.37 / Chapter 4.7 --- Simple Examples --- p.40 / Chapter 4.7.1 --- Oblique Incidence on Vacuum --- p.40 / Chapter 4.7.2 --- Oblique Incidence on Semi-Infinite Glass --- p.41 / Chapter 4.7.3 --- Normal Incidence on a Thin Gold Film --- p.41 / Chapter 5 --- A Tunable All-Direction Light Absorber --- p.43 / Chapter 5.1 --- Description of the Absorber --- p.44 / Chapter 5.2 --- Tunability --- p.45 / Chapter 5.3 --- Theoretical Understanding on the Results --- p.46 / Chapter 5.4 --- Other EM modes Involved --- p.49 / Chapter 5.5 --- Structural Flexibility --- p.54 / Chapter 6 --- Sample Preparation Techniques --- p.57 / Chapter 6.1 --- Interference Lithography --- p.57 / Chapter 6.1.1 --- Basic Principle of IL --- p.58 / Chapter 6.1.2 --- Experimental Setup for IL --- p.59 / Chapter 6.1.3 --- Experimental Procedures for IL --- p.60 / Chapter 6.1.4 --- Tuning the Period --- p.61 / Chapter 6.1.5 --- Tuning Grating Width --- p.62 / Chapter 6.1.6 --- Tuning the grating height --- p.64 / Chapter 6.2 --- Sputtering --- p.65 / Chapter 6.2.1 --- Description of Sputtering System --- p.65 / Chapter 6.2.2 --- Effect of Varying the Position on Sample Holder --- p.66 / Chapter 6.3 --- Chemical deposition of silver --- p.69 / Chapter 7 --- Sample Characterization Techniques --- p.72 / Chapter 7.1 --- Scanning Electron Microscope --- p.72 / Chapter 7.1.1 --- Grating width measurement --- p.72 / Chapter 7.1.2 --- Sidewall Coverage Measurement --- p.73 / Chapter 7.2 --- Thickness Measurement --- p.74 / Chapter 7.3 --- Reflectance Measurement --- p.75 / Chapter 7.3.1 --- Experimental Setup --- p.76 / Chapter 7.3.2 --- Use of Prism --- p.79 / Chapter 8 --- Experimental Realization of All-Direction Light Absorber --- p.82 / Chapter 8.1 --- Reflectance of Glass Substrate --- p.82 / Chapter 8.2 --- Planar Metal-SU8-Metal Systems --- p.87 / Chapter 8.3 --- SU8 Grating on Glass Substrate --- p.89 / Chapter 8.4 --- SU8 Grating on Gold Substrate --- p.92 / Chapter 8.4.1 --- Grating on a Thick Layer of Gold --- p.93 / Chapter 8.4.2 --- Grating on a Thin Layer of Gold --- p.93 / Chapter 8.5 --- Cavities-Embedded Systems and Future Work --- p.96 / Chapter 8.6 --- Summary and Future Experimental Work --- p.100 / Chapter 9 --- Conclusion --- p.102 / Chapter A --- Notes on Glass Cleaning --- p.104 / Chapter B --- An Experiment on Sidewall Coverage --- p.107 / Bibliography --- p.109

Thesis (Ph. D.)--Ohio State University, 2007. / Title from first page of PDF file. Includes bibliographical references (p. 361-380).

<p>Immobilization of different bio- and organic molecules on solid supports is fundamental within many areas of science. Sometimes, it is desirable to obtain a directed orientation of the molecule in the immobilized state. In this thesis, the copper (I) catalyzed Huisgen 1,3-dipolar cycloaddition, referred to as a “click chemistry” reaction, was explored as a means to perform directed immobilization of small molecule ligands on gold surfaces. The aim was to synthesize alkyne- and azide-terminated alkanethiols that would form well-organized self assembled monolayers (SAMs) on gold from the commercially available substances orthoethylene glycol and bromo alkanoic acid. N-(23-azido-3,6,9,12,15,18,21-heptaoxatricosyl)-n-mercaptododekanamide/hexadecaneamide (n = 12, 16) were successfully synthesized and allowed to form SAMs of different compositions to study how the differences in density of the functional groups on the surface would influence the structure of the monolayer and the click chemistry reaction. The surfaces were characterized by different optical methods: ellipsometry, contact angle goniometry and infrared reflection-absorption spectroscopy (IRAS). The click reaction was found to proceed at very high yields on all investigated surfaces. Finally, the biomolecular interaction between a ligand immobilized by click chemistry on the gold surfaces and a model protein (bovine carbonic anhydrase) was demonstrated by surface plasmon resonance using a Biacore system.</p>

Livet tas för givet av de flesta. Det finns däremot många som ägnar stora delar av sitt liv för att försöka lösa dess mysterier. En del av lösningen ligger i att förstå hur alla molekyler är sammanlänkade i det gigantiska nätverk som definierar den levande organismen. Under det senaste seklet har en hel del forskning utförts för att kartlägga dessa nätverk. Resultatet av dessa mödor kan vi se i de läkemedel som vi har idag och som har utvecklats för att bota eller åtminstone lindra olika sjukdomar och tillstånd. Dessvärre finns det fortfarande många sjukdomar som är obotliga (t.ex. cancer) och mycket arbete krävs för att förstå dem till fullo och kunna designa framgångsrika behandlingar. Arbetet i denna avhandling beskriver en analytisk plattform som kan användas för att effektivisera kartläggningsprocessen; protein-mikroarrayer. Mikroarrayer är ytor som har mikrometerstora (tusendels millimeter) strukturer i ett regelbundet mönster med möjligheten att studera många interaktioner mellan biologiska molekyler samtidigt. Detta medför snabbare och fler analyser - till en lägre kostnad. Protein-mikroarrayer har funnits i ungefär ett decennium och har följt i fotspåren av de framgångsrika DNA-mikroarrayerna. Man bedömer att protein-mikroarrayerna har en minst lika stor potential som DNA mikroarrayerna då det egentligen är mer relevant att studera proteiner, som är de funktionsreglerande molekylerna i en organism. Vi har i detta arbete tillverkat modellytor för stabil inbindning av proteiner, som lämnar dem intakta, funktionella och korrekt orienterade i ett mikroarray format. Därmed har vi adresserat ett stort problem med protein mikroarrays, nämligen att proteiner är känsliga molekyler och har i många fall svårt att överleva tillverkningsprocessen av mikroarrayerna. Vi har även studerat en metod att tillverka mikroarrayer av proteiner bundna till strukturer, som modellerats att efterlikna cellytor. Detta är särkilt viktigt eftersom många (hälften) av dagens (och säkerligen framtidens) läkemedel är riktade mot att påverka denna typ av proteiner och att studera dessa i sin naturliga miljö är därför väldigt relevant. I ett annat projekt har vi använt protein mikroarrayer för att detektera fyra vanliga droger (heroin, amfetamin, ecstasy och kokain). Detektionen baseras på användandet av antikroppar som lossnar från platser på ytan när de kommer i kontakt med ett narkotikum. Detta koncept kan enkelt utvecklas till att detektera mer än bara fyra droger. Vi har även lyckats att parallellt mäta förekomsten av en annan typ av förening på mikroarray ytan, nämligen det explosiva ämnet trinitrotoluen (TNT). Detta visar på en mångsidig plattform för detektionen av i princip vilken typ av farlig eller olaglig substans som helst - och på en yta! Vi föreställer oss därför att möjliga tillämpningsområden finns inom brottsbekämpning, i kampen mot terrorism och mot narkotikamissbruk etc. Mikroarrayerna har i denna avhandling utforskats med optiska metoder som tillåter studie av omärkta proteiner, vilket resulterar i så naturliga molekyler som möjligt. / Life is a thing taken for granted by most. However, it is the life-long quest of many to unravel the mysteries of it. Understanding and characterizing the incomprehensively complex molecular interaction networks within a biological organism, which defines that organism, is a vital prerequisite to understand life itself. Already, there has been a lot of research conducted and a large knowledge has been obtained about these pathways over, especially, the last century. We have seen the fruits of these labors in e.g. the development of medicines which have been able to cure or at least arrest many diseases and conditions. However, many diseases are still incurable (e.g. cancer) and a lot more work is still needed for understanding them fully and designing successful treatments. This work describes a generic analytical tool platform for aiding in more efficient (bio)molecular interaction mapping analyses; protein microarray chips. Microarray chips are surfaces with micrometer sized features with the possibility of studying the interactions of many (thousands to tens of thousands) (bio)molecules in parallel. This allows for a higher throughput of analyses to be performed at a reduced time and cost. Protein microarrays have been around for approximately a decade, following in the footsteps of the, so far, more successfully used DNA microarrays (developed in the 1990s). Microarrays of proteins are more difficult to produce because of the more complex nature of proteins as compared to DNA. In our work we have constructed model surfaces which allow for the stable, highly oriented, and functional immobilization of proteins in an array format. Our capture molecules are based on multivalent units of the chelator nitrilotriacetic acid (NTA), which is able to bind histidine-tagged proteins. Furthermore, we have explored an approach for studying lipid membrane bound systems, e.g. receptor-ligand interactions, in a parallelized, microarray format. The approach relies on the addressable, DNA-mediated adsorption of tagged lipid vesicles. In an analogous work we have used the protein microarray concept for the detection of four common narcotics (heroin, amphetamine, ecstasy, and cocaine). The detection is based on the displacement of loosely bound antibodies from surface array positions upon injection of a specific target analyte, i.e. a narcotic substance. The proof-of-concept chip can easily be expanded to monitor many more narcotic substances. In addition, we have also been able to simultaneously detect the explosive trinitrotoluene (TNT) along with the narcotics, showing that the chip is a versatile platform for the detection of virtually any type of harmful or illegal compound. This type of biosensor system is potentially envisaged to be used in the fight against crime, terrorism, drug abuse etc. Infrared reflection absorption spectroscopy together with ellipsometry has been used to characterize molecular layers used in the fabrication processes of the microarray features. Imaging surface plasmon resonance operating in the ellipsometric mode is subsequently used for functional evaluation of the microarrays using a well-defined receptor-ligand model system. This approach allows simultaneous and continuous monitoring of binding events taking place in multiple regions of interest on the microarray chip. A common characteristic of all the instrumentation used is that there is no requirement for labeling of the biomolecules to be detected, e.g. with fluorescent or radioactive probes. This feature allows for a flexible assay design and the use of more native proteins, without any time-consuming pretreatments.