Dissertations / Theses on the topic 'Surface plasmon resonance (SPR)'

Surface plasmon resonance (SPR) biosensors have attracted great attention in scientific research in the past three decades. Extensive studies on the immobilisation of biorecognition elements have been conducted in pursuit of higher sensitivity, but trialled formats have focussed on a thin layer modification next to the plasmon film, which usually requires in situ derivatization. This thesis investigates an 'off-chip' immobilisation strategy for SPR biosensing using silica particles and considers the implications of a particle-modified evanescent field on the signal amplitude and kinetics, for an exemplar affinity binding between immobilised IgG and its anti-IgG complement. Submicron silica particles were synthesized as carriers for the bio-recognition elements. They were then immobilised to form a sub-monolayer on the gold film of an SPR biosensor using two methods: thiolsilane coupling and physical adsorption aided by mechanical pressure. The bio-sensitivity towards an antigen/antibody interaction was lower than an SPR biosensor with an alkanethiolate SAM due to the difference in ligand capacity and position in the evanescent field. The binding kinetics of antigen/antibody pair was found to follow the Langmuir model closely in a continuous flow configuration but was heavily limited by the mass transport from the bulk to the sensor surface in a stop-flow configuration. A packed channel configuration was designed with larger gel particles as ligand carriers, packed on top of a gold film to create a column-modified SPR biosensor. This sensor has comparable bio-sensitivity to the previous sub-monolayer particle-modified systems, but the binding and dissociation of the analyte was heavily dependent on mass transport and binding equilibria across the column. A bi-directional diffusion mechanism was proposed based on a two-compartment mass transport model and the expanded model fitted well with the experimental data. The column-modified sensor was also studied by SPR imaging and analyte band formation was observed and analysed. Using the lateral resolution, a multiplexing particle column configuration was explored, and its potential in distinguishing a multicomponent analyte.

En terme de performance, le biocapteur idéal doit avoir très grande sensibilité, basse limite de détection et temps d’analyse qui est extrêmement court. Les biocapteurs sans marquage à base de résonance de plasmons de surface (biocapteurs SPR) possèdent naturellement le temps d’analyse le plus court parmi différent types de biocapteurs. Leur limite de détection n’est cependant pas la plus impressionnante. Il y a donc un besoin pour augmenter considérablement la sensibilité intrinsèque des biocapteurs SPR afin de permettre de plus basses limites de détection. Quelques approches pour exalter la sensibilité optique des biocapteurs SPR dans la configuration « traditionnel » de Krestchmann telles que film SPR bimétallique, plasmons à longues portées et détection dans l’infrarouge proche sont examinées dans ce travail. Des configurations « non traditionnelles » comme guides optiques planaires avec couplage par réseau et structures sub-longueur d’ondes ont été aussi théoriquement étudiées. Nouvelle stratégie de fonctionnalisation de surface à base de graphène qui augmente la sensibilité de reconnaissance biomoléculaire et peut être appliquée à quasiment toute structure SPR a été également démontrée
In terms of performance, the ideal biosensor should have high sensitivity, low limits of detection, and extremely short analysis time. Label-free surface plasmon resonance (SPR) biosensors naturally offer the shortest analysis time compared to other types of biosensors. On the other hand, the limits of detection of SPR biosensors are not the most impressive. The inherent sensitivity of SPR biosensors thus needs to be significantly improved to allow lower limits of detection. Several approaches for the enhancement of optical sensitivity of SPR biosensors in the “traditional” attenuated total reflection (ATR) Kretschmann configuration such as the use of bimetallic SPR film, long-range surface plasmons, and near-infrared operating wavelength have been investigated in this work. In addition, some “non traditional” configurations for SPR biosensors including grating-coupled planar optical waveguides and arrays of sub-wavelength structures have been theoretically studied. Novel graphene-based surface functionalization strategy with enhanced biorecognition sensitivity that can be applied to virtually any SPR structure has also been demonstrated

Surface plasmon waves are transverse magnetic electromagnetic waves propagating along a dielectric-metal interface. These waves can be excited by resonant absorption of electromagnetic radiation leading to surface plasmon resonance (SPR) at the interface. The resonance is characterised by a reduction in the intensity of the reflected light at the interface due to strong coupling of incident optical radiation to surface plasmons. This gives rise to a minimum at a sharply defined angle of incidence, referred to as SPR angle or plasmon angle. The phenomenon of SPR has been extensively used in the past to develop reflective type optical devices for sensing applications on account of the high dielectric function dependent sensitivity of the SPR angle. Basically, devices which exhibit this phenomenon have a structure consisting of a metal film sandwiched between two dielectrics. The reflectivity of such a device is theoretically modelled based on either theory of thin films (Fresnel's model) or theory of resonance (Lorentzian model). These models have very effectively predicted the behaviour of such devices based on the shift in SPR angle due to the dielectric function variations. We have been investigating the SPR device for intensity based metrological applications utilising its high angular sensitive reflectivity, with fixed SPR angle. In these intensity based applications or measurements, direct and simple expressions connecting intensity variation to angular change are unavailable in the literature and quantitative estimation or data inversion is based on either curve fitting or iterative methods. Fresnel and Lorentzian models have commonly been used in the experiments but data inversion through the Fresnel model is computationally complex and the Lorentzian model, although less complicated, gives erroneous results due to its approximate nature. In order to obtain a simple expression between intensity variation and the angular change, we have re-looked at the two existing models in order to derive an expression which has the simplicity of the Lorentzian model and the accuracy of the Fresnel model in the experiments with fixed plasmon angles. These efforts have been particularly directed to understand the relationship between intensity variation and meteorologically important properties of such devices. This thesis is an attempt to summarize the computational results which have led us to some novel experimental methodologies which have been used to exploit these devices for inverse type, illumination specific, SPR based applications. The work presented in this thesis is organised in six chapters. Chapter 1, gives an overview of optical sensing, theory of surface plasmons, excitation schemes for surface plasmons, development of the SPR device and its characterisation. It also includes a brief literature review in the area of surface plasmon resonance, covering both the theoretical and experimental aspects. The objectives of the work and the scope of the thesis are also presented. Chapter 2 presents the existing models of SPR device, based on Fresnel's and the Lorentzian models. These models allow reflectance calculations from knowledge of either the optical parameters that describe the layers or the parameters of the waves that propagate through them. Using these models, the inverse problem of estimating either the angle of incidence or the optical constants of the layers of the sensors utilizing the intensity based measurements is generally difficult. In order to solve this problem where the plasmon angles are fixed, a modified formalism for the angle scanned SPR spectrum of a three-layered SPR sensor is presented in this chapter. The new formalism regroups the wave vector parameters of Lorentzian resonance theory into a set of non-dimensional parameters 1, 4K and R. The new reflectivity index (1), which is the ratio of reflectance to the absorptance, has been introduced to help explain the physical processes underlying the device operation in the high sensitivity region of the characteristics. The parameter 4Kis a constant of the device and it depends on the dielectric constants of the device. This is a new SPR index and is identified at a point where reflectance and absorptance match. Parameter R is related to the loss mechanisms in the device and will be explained in detail in Chapter 3. This simple model links the new reflectivity index (1) to the angular detune from SPR angle (ΔƟ) and it brings out a parabolic variation of ΔƟ with 1. In this chapter the mathematical derivation of the proposed model is presented and the significance of the new parameters 1, 4Kand Rare discussed. Chapter 3 evaluates the characteristic nature of errors associated with the predictions from the proposed model and presents methods for neutralizing them. It is demonstrated with the help of the function K which is linearly dependant on 1, that the proposed model predicts the reflectance from the wave vector parameters as accurately as the Fresnel's model. This R parameter explains the slowly varying nature of the radiative loss with the angle of incidence and this variation contributes significantly to the SPR characteristics. As a consequence, it is found that the SPR characteristics can be represented as a sum of two primary functions which are parabolic and linear, respectively, and this leads to the easy explanation of the SPR characteristics. The present chapter also discusses a new observation that the angle-scanned SPR spectrum can be accurately described using a straight line in intercept form. The intercept value depends on 4Kand the slope depends on K. In addition to this, this chapter discusses practical methods for estimation of the intercept and the slope of such a straight line which are functions of the key wave vector parameters. A detailed discussion on the proposed model highlighting its advantages for inverse type, illumination specific, SPR-based applications with fixed SPR angle is also presented. Chapter 4 describes the applications of the proposed model for optical constant measurements. The first part highlights a new approach for the determination of the dielectric constants of the metal film used for the optimised- or nearly-optimised SPR sensors using the proposed model. In the complex dielectric constant, the real part is calculated from the SPR angle and the imaginary part from 4K. A discussion on the dielectric constant study of silver and gold metal film is presented. The advantages of the proposed approach such as its simplicity and direct methodology are then discussed. The second part of the chapter also proposes a new approach to carry out measurements on the absorbance of the medium with enhanced sensitivity utilising the parameter 4K It describes a computational study on the variation of 4K values with the dielectric function and highlights the relationship of 4K variation due to the imaginary part of the dielectric function (absorption) of the samples. The physical processes causing a change in the value of 4Kdue to absorption is also discussed along with some computational results. Chapter 5 reports the study carried out to bring out the importance of the new index,4K in metrological applications. Based on the new model, the effect of the laser beam divergence on SPR curve is studied. This chapter first of all discusses the design of the SPR device and the new methods for the development and characterisation of such a device. Details of the experimental procedure for laser divergence evaluation are proposed along with some of the significant computational results. Furthermore, a few applications such as focal length measurement of optical lenses, micro-displacement measurement based on the divergence of the laser beam are also reported. Since the SPR characteristics can be represented easily using the new model, the angular dependent intensity variation can be utilised for some metrological applications with simple data processing. In this context, the high angular sensitivity of the SPR device is studied and some applications such as micro-displacement measurement, pressure measurement and optical wedge angle measurement are included to highlight the above advantages. The last chapter, Chapter 6, gives a summary and conclusions of the work presented in the thesis. The scope for future investigations is also included in this chapter.

Surface plasmon waves are transverse magnetic electromagnetic waves propagating along a dielectric-metal interface. These waves can be excited by resonant absorption of electromagnetic radiation leading to surface plasmon resonance (SPR) at the interface. The resonance is characterised by a reduction in the intensity of the reflected light at the interface due to strong coupling of incident optical radiation to surface plasmons. This gives rise to a minimum at a sharply defined angle of incidence, referred to as SPR angle or plasmon angle. The phenomenon of SPR has been extensively used in the past to develop reflective type optical devices for sensing applications on account of the high dielectric function dependent sensitivity of the SPR angle. Basically, devices which exhibit this phenomenon have a structure consisting of a metal film sandwiched between two dielectrics. The reflectivity of such a device is theoretically modelled based on either theory of thin films (Fresnel's model) or theory of resonance (Lorentzian model). These models have very effectively predicted the behaviour of such devices based on the shift in SPR angle due to the dielectric function variations. We have been investigating the SPR device for intensity based metrological applications utilising its high angular sensitive reflectivity, with fixed SPR angle. In these intensity based applications or measurements, direct and simple expressions connecting intensity variation to angular change are unavailable in the literature and quantitative estimation or data inversion is based on either curve fitting or iterative methods. Fresnel and Lorentzian models have commonly been used in the experiments but data inversion through the Fresnel model is computationally complex and the Lorentzian model, although less complicated, gives erroneous results due to its approximate nature. In order to obtain a simple expression between intensity variation and the angular change, we have re-looked at the two existing models in order to derive an expression which has the simplicity of the Lorentzian model and the accuracy of the Fresnel model in the experiments with fixed plasmon angles. These efforts have been particularly directed to understand the relationship between intensity variation and meteorologically important properties of such devices. This thesis is an attempt to summarize the computational results which have led us to some novel experimental methodologies which have been used to exploit these devices for inverse type, illumination specific, SPR based applications. The work presented in this thesis is organised in six chapters. Chapter 1, gives an overview of optical sensing, theory of surface plasmons, excitation schemes for surface plasmons, development of the SPR device and its characterisation. It also includes a brief literature review in the area of surface plasmon resonance, covering both the theoretical and experimental aspects. The objectives of the work and the scope of the thesis are also presented. Chapter 2 presents the existing models of SPR device, based on Fresnel's and the Lorentzian models. These models allow reflectance calculations from knowledge of either the optical parameters that describe the layers or the parameters of the waves that propagate through them. Using these models, the inverse problem of estimating either the angle of incidence or the optical constants of the layers of the sensors utilizing the intensity based measurements is generally difficult. In order to solve this problem where the plasmon angles are fixed, a modified formalism for the angle scanned SPR spectrum of a three-layered SPR sensor is presented in this chapter. The new formalism regroups the wave vector parameters of Lorentzian resonance theory into a set of non-dimensional parameters 1, 4K and R. The new reflectivity index (1), which is the ratio of reflectance to the absorptance, has been introduced to help explain the physical processes underlying the device operation in the high sensitivity region of the characteristics. The parameter 4Kis a constant of the device and it depends on the dielectric constants of the device. This is a new SPR index and is identified at a point where reflectance and absorptance match. Parameter R is related to the loss mechanisms in the device and will be explained in detail in Chapter 3. This simple model links the new reflectivity index (1) to the angular detune from SPR angle (ΔƟ) and it brings out a parabolic variation of ΔƟ with 1. In this chapter the mathematical derivation of the proposed model is presented and the significance of the new parameters 1, 4Kand Rare discussed. Chapter 3 evaluates the characteristic nature of errors associated with the predictions from the proposed model and presents methods for neutralizing them. It is demonstrated with the help of the function K which is linearly dependant on 1, that the proposed model predicts the reflectance from the wave vector parameters as accurately as the Fresnel's model. This R parameter explains the slowly varying nature of the radiative loss with the angle of incidence and this variation contributes significantly to the SPR characteristics. As a consequence, it is found that the SPR characteristics can be represented as a sum of two primary functions which are parabolic and linear, respectively, and this leads to the easy explanation of the SPR characteristics. The present chapter also discusses a new observation that the angle-scanned SPR spectrum can be accurately described using a straight line in intercept form. The intercept value depends on 4Kand the slope depends on K. In addition to this, this chapter discusses practical methods for estimation of the intercept and the slope of such a straight line which are functions of the key wave vector parameters. A detailed discussion on the proposed model highlighting its advantages for inverse type, illumination specific, SPR-based applications with fixed SPR angle is also presented. Chapter 4 describes the applications of the proposed model for optical constant measurements. The first part highlights a new approach for the determination of the dielectric constants of the metal film used for the optimised- or nearly-optimised SPR sensors using the proposed model. In the complex dielectric constant, the real part is calculated from the SPR angle and the imaginary part from 4K. A discussion on the dielectric constant study of silver and gold metal film is presented. The advantages of the proposed approach such as its simplicity and direct methodology are then discussed. The second part of the chapter also proposes a new approach to carry out measurements on the absorbance of the medium with enhanced sensitivity utilising the parameter 4K It describes a computational study on the variation of 4K values with the dielectric function and highlights the relationship of 4K variation due to the imaginary part of the dielectric function (absorption) of the samples. The physical processes causing a change in the value of 4Kdue to absorption is also discussed along with some computational results. Chapter 5 reports the study carried out to bring out the importance of the new index,4K in metrological applications. Based on the new model, the effect of the laser beam divergence on SPR curve is studied. This chapter first of all discusses the design of the SPR device and the new methods for the development and characterisation of such a device. Details of the experimental procedure for laser divergence evaluation are proposed along with some of the significant computational results. Furthermore, a few applications such as focal length measurement of optical lenses, micro-displacement measurement based on the divergence of the laser beam are also reported. Since the SPR characteristics can be represented easily using the new model, the angular dependent intensity variation can be utilised for some metrological applications with simple data processing. In this context, the high angular sensitivity of the SPR device is studied and some applications such as micro-displacement measurement, pressure measurement and optical wedge angle measurement are included to highlight the above advantages. The last chapter, Chapter 6, gives a summary and conclusions of the work presented in the thesis. The scope for future investigations is also included in this chapter.

Current major demands in SPR sensor development are system miniaturization and throughput improvement. Structuring an array of integrated optical SPR sensor heads on a semiconductor based optoelectronic platform could be a promising solution for those issues, since integrated optical waveguides have highly miniaturized dimension and the optoelectronic platform enables on-chip optical-to-electrical signal conversion. Utilizing a semiconductor based platform to achieve optoelectronic functionality poses requirements to the senor head; the sensor head needs to have reasonably small size while it should have reasonable sensitivity and fabrication tolerance. This research proposes a novel type of SPR sensor head and demonstrates a fabricated device with an array of integrated optical SPR sensor heads endowed with optoelectronic functionality. The novel integrated optical SPR sensor head relies on mode conversion efficiency for its operational principle. The beauty of this type of sensor head is it can produce clear contrast in SPR spectrum with a highly miniaturized and simple structure, in contrast to several-millimeter-scale conventional absorption type or interferometer type sensor heads. The integrated optical SPR sensor with optoelectronic functionality has been realized by structuring a dielectric waveguide based SPR sensor head on a photodetector-integrated semiconductor substrate. A large number of unit sensors have been fabricated on a substrate with a batch fabrication process, which promises a high throughput SPR sensor system or low-priced disposable sensors.
Ph.D.
Optics and Photonics
Optics and Photonics
Optics PhD

Surface plasmon waves are TM polarized charge density waves that propagate at the interface of two media with real dielectric constants of opposite sign (i.e. liquid dielectric and certain metals). Surface plasmon resonance (SPR) sensors use these waves to detect refractive index changes adjacent to the metal layer. Refractive index changes arise from the binding of an analyte (e.g. a target molecule, protein, or bacterium) to the functionalized metal layer or from interfering effects such as changes in solution index. Standard, single channel SPR sensors cannot differentiate these two effects as their design allows only one mode to be coupled. This novel self-referencing technique employs two surface plasmon modes to simultaneously measure surface binding and solution refractive index. Dual surface plasmon modes are achieved by matching the refractive indices on either side of the metal film. The two modes generated - symmetric, long-range surface plasmon (LRSP) and anti-symmetric, short-range surface plasmon (SRSP) - have different field profiles and hence assist in differentiating solution refractive index changes from surface layer formation. Amorphous Teflon, with a refractive index close to water, is chosen as the buffer layer and gold is chosen as the metal layer. Magnesium fluoride, with a higher index than Teflon, is used as the buffer layer when using ethanol as the base solution. The sensor operation was optimized through simulations to yield higher sensitivity, lower reflectivity and resonances within the spectrometers range. Optimization results showed good performance over a wide range for Teflon, MgF2 and gold thicknesses which helped in the fabrication of the sensor. Demonstration of self-referencing operation was done through two different sets of experiments: (1) formation of an alkanethiol self-assembled monolayer on gold in the presence of ethanol and methanol solutions having different refractive indices and (2) streptavidin-biotin binding with solutions of different NaCl concentration and thus different refractive indices. In both these experiments, the resonance wavelengths were accurately predicted, reflectivity varied by 10-15% and sensitivity by 25% from that of the simulated values.

Surface plasmons are bound TM polarized electromagnetic waves that propagate along the interface of two materials with real dielectric constants of opposite signs. Surface plasmon resonance (SPR) sensors make use of the surface plasmon waves to detect refractive index changes occurring near this interface. For sensing purposes, this interface typically consists of a metal layer, usually gold or silver, and a liquid dielectric. SPR sensors usually measure the shift in resonance wavelength or resonance angle due to index changes adjacent to the metal layer. However this restricts the limit of detection (LOD), as the regions of low slope (intensity vs. wavelength or angle) in the SPR curve contain little information about the resonance. This work presents the technique of tunable laser interrogation of SPR sensors. A semiconductor laser with a typical lasing wavelength of 650nm was used. A 45nm gold layer sputtered on a BK7 glass substrate served as the sensor. The laser wavelength is tuned to always operate in the region of highest slope by using a custom-designed LabVIEW program. It is shown that the sensitivity is maximized and LOD is minimized by operating around the region of high slope on the SPR curve.

Type 2 diabetes or adult onset diabetes, has been a global epidemic for the past two decades, and the number of new cases accelerates every year. Insulin resistance is one of the major factors behind this, wherein the insulin receptor, which signals to regulate glucose levels, based on the hormone insulin, loses its sensitivity. Obesity is one other major concern which is caused due to the improper balance between the caloric intake and the energy utilized. Gastric bypass surgeries (GBP) are performed to avert obesity. However, a beneficial side-effect is that the state of insulin resistance is reset to near baseline levels within a few days after the procedure. The reason behind this remains unexplained, with possible humoral effects, hypothesized to occur after the bariatric procedure. In this work, high-five insect cell line was utilized to recombinantly produce full length insulin receptors (IR). However commercially sourced IR ectodomains (eIR – soluble version of the full length IR with the completely extracellular α subunits along with extracellular and transmembrane regions of the β subunit), were used to study the interaction. Measuring the kinetics of IR-insulin interactions is critical to improving our understanding of this disease. In this study, a multiplex surface plasmon resonance (SPR) assay was developed for studying the interaction between insulin and the eIR. A scaffold approach was used in which anti-insulin receptor monoclonal antibody 83–7 (Abcam, Cambridge, UK) was first immobilized on the SPR sensorchip by amine coupling, followed by eIR capture. The multiplex SPR system (ProteOn XPR36TM, Bio-Rad Laboratories, Hercules, CA) enabled measurement of replicate interactions with a single, parallel set of analyte injections, whereas repeated regeneration of the scaffold between measurements caused variable loss of antibody activity. The main approach was to replicate the physiological IR-insulin interaction using this assay. It was also observed that insulin at higher concentrations tend to form dimers and hexamers in solution. This was tested using size exclusion chromatography analysis and proved to be true. Therefore an alternative analyte with the similar binding properties and affinity of insulin and at the same time with reduced self- association characteristics was explored. Lispro, the analogue of insulin with reduced self-association properties (generated by swapping of residue 28 and 29 with Lys and Pro respectively) was finally used to study the interaction with eIR. Interactions between recombinant human insulin with eIR-A (A isoform of the insulin receptor ectodomain) followed a two-site binding pattern (consistent with the literature), with a high-affinity site (dissociation constant KD1 = 38.1 ± 0.9 nM) and a low-affinity site (KD2 = 166.3 ± 7.3 nM). The predominantly monomeric insulin analogue Lispro had corresponding dissociation constants KD1 =73.2 ± 1.8 nM and KD2 =148.9 ± 6.1 nM, but the fit to kinetic data was improved when conformational change factor was included in which the high-affinity site was converted to the low-affinity site. Kinetics of interaction of insulin with eIR-A and eIR-B isoforms were then compared. eIR-A bound insulin with apparently higher affinity (with both the binding sites) when compared with eIR-B. This was again consistent with literature that IR-A had two-fold higher affinity for binding insulin than IR-B. The assay was further extended to study the effect of external factors such as glucose, visfatin on this interaction. Glucose (the main biomolecule which is regulated by the IR-insulin interaction) was tested, if it had any direct effect on the interaction. It was observed that glucose did not have any effect on eIR-insulin interactions. Visfatin, an adipocytokine which has been highly debated in literature for its insulin mimetic effects and IR binding properties, was then tested. The standard assay did not provide much insights as the reference channel immobilized with 83-7 monoclonal antibody to the receptor had much affinity for visfatin, leading to non-specific binding and negative responses. Therefore, in an alternative methodology was used - visfatin, Lispro and insulin were immobilized on separate channels along with bovine serum albumin immobilized on reference channel and eIR isoforms used as analyte to study the effect of visfatin on IR. This study showed that visfatin, a higher molecular weight protein compared to insulin, bound both the eIR isoforms. This is consistent with literature that visfatin binds IR at a site distinct from insulin, but the assay described here could not confirm the fact that it mimicked the signalling carried out by IR-insulin binding. Further studies are required to interpret the kinetics of visfatin-eIR interaction. To my knowledge, this is the first SPR assay developed to study eIR-insulin interactions in real-time. This could potentially be extended to study the interaction of insulin with full length insulin receptors and the effect of humoral and other external factors on the interaction, without the need for insulin labelling.

Surface plasmon resonance (SPR) sensors using multiwavelength light coupling are investigated to probe changes in refractive index that occur as a result of chemical or biochemical processes. Traditional SPR sensors have used angle modulation to facilitate detection at the sensor surface; however, the multiwavelength approach is novel and brings new functionality to SPR sensors. The multiwavelength sensors are constructed on both fiber optic and bulk waveguides such as prisms. A thin metal film is deposited on the waveguide surface to support the surface plasmon (SP) mode. The evanescent field produced by light propagating through the waveguide can be coupled into the surface plasmon mode thus attenuating the transmitted light. This coupling is dependent upon phase matching between the light wavevector and the surface plasmon wavevector. The wavevectors are directly related to the wavelength of light, thickness of analyte on the sensor surface and the refractive index of the analyte. As these parameters change, the light output from the sensor will be affected. Other thin films can be subsequently deposited on the metal to functionalize the sensor surface for a particular analyte of interest. A theoretical background and details of the sensor construction is given. The developed sensors are tested in a variety of application systems. Experimental results for refractive index sensing in bulk liquid applications is shown. Observed sensitivity approaches that of conventional SPR techniques. Alkyl-thiol monolayer systems are studied to investigate kinetics of formation and the thickness resolution of the sensor. A biochemical system is investigated to compare the sensors with other immunoassay techniques. Ionic self-assembled monolayer (ISAM) systems are investigated to probe structure and determine their usefulness as an immobilization layer for biochemical species. A mathematical model based on Fresnel reflection equations is developed to predict sensor response. This model can be used to selectively vary sensor parameters to optimize the response for a specific analyte system or to calculate system parameters based on experimental results. Results from the various experiments are compared with the model. Experimental results and interpretations are discussed along with future work and potential improvements. Classical SPR sensors are also discussed along with comparisons with the multiwavelength sensors. Future improvements to SPR sensors design are considered, as is the application of the technology to high-throughput drug screening for pharmaceuticals.
Ph. D.

Fragment based drug discovery (FBDD) has been applied to two protease drug targets, MMP-12 and HIV-1 protease. The primary screening and characterization of hit fragments were performed with surface plasmon resonance -technology. Further evaluation of the interaction was done by inhibition studies and in one case with X-ray crystallography. The focus of the two projects was different. Many MMP inhibitors contain a strong zinc chelating group, hydroxamate, interacting with the catalytic zinc atom. This strategy may be the cause for the low specificity of MMP inhibitors. Using FBDD we found a fragment with an unusual strong affinity for MMP-12. An inhibition assay confirmed that it was an inhibitor but indicated a stoichiometry of 2:1. Crystallography data revealed that an adduct of the fragment was bound in the active site, with interactions both with the catalytic zinc and the S1’ pocket. This may present a new scaffold for MMP-12 inhibitors. For HIV-1 protease the focus was on identifying inhibitors not sensitive to current resistance mutations. A fragment library for screening with SPR-technology was designed and used for screening against wild type enzyme and three variants with resistance mutations. Many of the hits were promiscuous but a number of fragments with possible allosteric inhibition mechanism were identified. The temperature dependency of the dissociation rate and reported resistance mutations was studied with thermodynamics. A good, but not perfect correlation was found between resistance and both the dissociation data and the free energy for dissociation compared to data from wild type enzyme. However, the type of mutation also influenced the results. The flap mutation G48V displayed thermodynamic profiles not completely correlating with resistance. It was found that dissociation rate and thermodynamics may complement each other when studying resistance, but only one of them may not be enough.

Surface-plasmon-resonance (SPR) sensors are widely used in biological, chemical, medical, and environmental sensing. This dissertation describes the design and development of dual-mode, self-referencing SPR sensors supporting two surface-plasmon modes (long- and short-range) which can differentiate surface binding interactions from bulk index changes at a single sensing location. Dual-mode SPR sensors have been optimized for surface limit of detection (LOD). In a wavelength interrogated optical setup, both surface plasmons are simultaneously excited at the same location and incident angle but at different wavelengths. To improve the sensor performance, a new approach to dual-mode SPR sensing is presented that offers improved differentiation between surface and bulk effects. By using an angular interrogation, both surface plasmons are simultaneously excited at the same location and wavelength but at different angles. Angular interrogation offers at least a factor of 3.6 improvement in surface and bulk cross-sensitivity compared to wavelength-interrogated dual-mode SPR sensors. Multi-mode SPR sensors supporting at least three surface-plasmon modes can differentiate a target surface effect from interfering surface effects and bulk index changes. This dissertation describes a tri-mode SPR sensor which supports three surface plasmon resonance modes at one single sensing position, where each mode is excited at a different wavelength. The tri-mode SPR sensor can successfully differentiate specific binding from the non-specific binding and bulk index changes.

The Microelectronics Group has been researching sensors useful for detecting and quantifying events in biological molecular chemistry, for example, binding events. Our previous research has been based primarily on quartz resonators. This thesis describes the results of our initial research of Surface Plasmon Resonance (SPR) based technology. This study contains the design and implementation of a fully functional SPR biosensor with detailed disclosure of monolayer construction, digital hardware interfaces and software algorithms for process the SPR sensors output. An antibody monolayer was constructed on the biosensor surface with the goal of setting the strengths, weaknesses and limitation of measuring molecular events with SPR technology. We documented several characteristics of molecular chemistry that directly effect any measurements made using Surface Plasmon Resonance technology including pH, free ions, viscosity and temperature. Furthermore, the component used in our study introduced additional limitations due to wide variations amongst parts, the constraint of a liquid medium and the large surface area used for molecular interrogation. We have identified viable applications for this sensor by either eliminating or compensating for the factors that affect the measured results. This research has been published at the inaugural IEEE sensors conference and to our knowledge is the first time a biosensor has been constructed by attaching a sensor to a PDA and performing all signal processing, waveform analysis and display in the PDAs core processor.

The thesis investigates the realization of all-optical sensors for the detection of chemicals and bio-chemicals by exploiting the properties of surface plasma waves (or plasmons) excited at a dielectric-metal interface, the so called phenomenon of surface plasmon resonance (SPR). SPR occurs for light with suitable wavelength, incidence and polarization and manifests itself as a strong attenuation of the light reflection coefficient at the metal-dielectric interface. Supposing to use a broadband light source for the interrogation, this turns out in a deep and narrow notch in the reflected spectrum, the position of which is strongly dependent on the refractive index of the substance (the analyte) in contact with the metal layer. These sensors are characterized by very high sensitivity and, after proper functionalization, are therefore used in chemical and biochemical analysis to detect ppb (part-per-billion) concentrations of specific substances, such as pollutants in water. A further reason of interest is the possibility to conduct label-free analyses, without the use of other chemicals to make the analyte detectable. The construction parameters (e.g. metal used, layer thickness, and incidence angle, just to name a few) play a key role in determining the performance of these sensors. Therefore, in the first part of the thesis a mathematical model is introduced to allow running parametric simulations to optimize the layout according to the different configurations and applications. Then, based on the indications obtained from the simulations, some prototypes both in bulk optic (i.e. using prisms-based setups) and in optical fiber configurations have been realized and fully characterized to validate the implemented models. Optical fiber based sensors are particularly interesting for their small size that makes them well suited in all those applications where it is required the use of a compact, lightweight and minimally invasive system. For this reason, the fiber optic SPR sensor solution is often taken as the reference sensing system throughout the thesis. In a second part of the thesis, in view of long-term monitoring applications, the most critical parameters affecting the sensor resolution have been identified and analyzed in detail. These are: i) the stability of the optical source used to interrogate the sensor; ii) the influence of misalignments and other mechanical instabilities; iii) the effect of temperature fluctuations. As for the optical source stability, the most common source types used in practical setups (halogen lamp, super-continuum laser and SLED) have been measured, and a method to compare their long-term fluctuations and subsequent influence on the sensor performance has been devised. Similar approach based on the analysis of repeated experimental results has been applied also to evaluate the impact of the main mechanical parameters, such as the light beam angle of incidence, both intentionally and unintentionally variable, respectively in the bulk optic setup or in the fiber-based setup. The latter, in particular, is very relevant in the development of fiber sensing probes that to be disposable need to be low cost, and thus they make use of cheap connectors with poor repeatability. Another key issue is the effect of temperature. Indeed, since the refractive index is also function of the temperature and a SPR sensor basically detects changes in the refractive index, if the whole measuring system is not kept at a constant temperature, its drift induces a shift in the position of the plasmon resonance; and this could be erroneously interpreted as a variation in the concentration of the analyte. The solution widely used to reduce this drawback is to stabilize the temperature (typically using Peltier modules) and insert the whole sensing part in robust chassis; this, however, makes the instrument bulky and suitable for lab use only, and definitely not for portable monitoring systems. To overcome these limitations, a new internally compensated sensor configuration has been studied and its behavior assessed through some experiments. In the final part of the thesis all the analyzed aspects and developed solutions are applied to a feasibility study of SPR fiber sensor probes for Continuous Glucose Monitoring application (CGM), a topic of high relevance considering that diabetes constitutes one of the most common diseases, affecting more than 350 million people worldwide, corresponding to more than 8% of the adult population.

A novel localized surface plasmon resonance (LSPR) sensor that differentiates between background refractive index changes and surface-binding of a target analyte (e.g. a target molecule, protein, or bacterium) is presented. Standard, single channel LSPR sensors cannot differentiate these two effects as their design allows only one mode to be coupled. This novel technique uses two surface plasmon modes to simultaneously measure surface binding and solution refractive index changes. This increases the sensitivity of the sensor. Different channels or modes can be created in sensors with the introduction of gold nanospheres or gold nanorods that act as receptor mechanisms. Once immobilization was achieved on gold nanospheres, the technique was optimized to achieve the same immobilization for gold nanorods to get the expected dual mode spectrum. Intricate fabrication methods are illustrated with using chemically terminated self assembled monolayers. Then the fabrication process advances from chemically silanized nanoparticles, on to specific and systematic patterns generated with the use of Electron Beam Lithography. Comparisons are made within the different methods used, and guidelines are set to create possible room for improvement. Some methods implemented failed, but there was a lot to learn from these unsuccessful outcomes. Finally, the applications of the dual mode sensor are introduced, and current venues where the sensors can be used in chemical and biological settings are discussed.

New methods and technology are needed to detect biological agents that threaten the health of humans and domestic animals. The bacterium Bacillus anthracis, causal agent of anthrax, has been used as a biological warfare agent. Here, we extend the work of Chinowksy et al. (2007) to the detection of a surrogate of B. anthracis, B. globigii (also known as B. atrophaeus, B. subtilis var. niger, B. subtilis var. subtilis) in a mixed sample containing two different species of Bacillus using a portable surface plasmon resonance (SPR) biosensor (SPIRIT 4.0, Seattle Sensor Systems). Two methods (direct capture and antibody injection) were used to determine the limit of detection for spores of B. globigii and to detect spores of B. globigii in a mixed sample containing at least one other Bacillus spp. Spores of B. globigii were detected on freshly coated sensors (not previously exposed to spores) with direct capture at a minimum concentration of 10^7 spores/mL, and with antibody injection at a concentration of 10^5 spores/mL. Spores of B. globigii were also detected when mixed with B. pumilus spores in the same sample at equal concentrations (107 spores/mL) using antibody injection. An SPR method using synthetic miRNA was adapted to the portable SPR unit (SPIRIT), and preliminary experiments suggested that the target sequence could be detected. SPR methods using nucleic acids have an exciting future in the detection of biological agents, such as B. anthracis. With the availability of portable instrumentation to accurately detect biological warfare agents such as B. anthracis, emergency responders can implement emergency protocols in a timely fashion, limiting the amount of people and domestic animals exposed.
Master of Science

Electron-excited surface plasmon resonance (eSPR) is investigated for potential use in biosensors. Optical SPR sensors are commercially available at present and these sensors are extremely sensitive, but have the tendency to be relatively large, expensive, and ignore the potentials of microelectronic technology. By employing the use of various microelectronic and nanotechnology principles, the goal is to eventually design a device that exploits the eSPR phenomenon in order to make a sensor which is siginificantly smaller in size, more robust, and cheaper in cost.

A capture step with protein A is the most common purification step in the downstream purification process of monoclonal antibodies. It is therefore of great importance to increase the knowledge of the interactions involved in this purification technique. The purpose of this master thesis project was to determine the affinity of protein A domains to IgG subclasses by surface plasmon resonance (SPR).

Besides the five homologous IgG-binding protein A domains (E, D, A, B, and C) an engineered domain, similar to domain B and used in the protein A media MabSelect Sure™ (GE Healthcare) was included in the study. The domains were expressed in E.coli, affinity purified and immobilized onto sensor chip surfaces by amine coupling. The antibodies used in the interaction analyses were of the human IgG subclasses 1, 2, 3, and 4. Affinity determination was performed by kinetic analyses with the SPR-biosensor Biacore™ 2000.

All human IgG subclasses except IgG3 were shown to bind to all protein A domains including the monomer of the SuRe ligand. The equilibrium constants, KD-values, obtained were all in the low nanomolar range. For IgG1 and IgG4, no significantly differences in the affinity to any of the protein A domains were found, except for domain E where there might be quality issues of the prepared domain. Furthermore, a detected quality issue with the commercial IgG2 made it impossible to determine the KD-values for this subclass with any reliability.

In this project a method based on surface plasmon resonance has been developed for determining the concentration of several His-tagged proteins in complex solutions. It showed large dynamic range, no measureable non-specific binding and high sensitivity (with linear range around 0.1–10 μg/ml depending on the proteins). The method showed a low variation when checked on MBP-His during an extended time period. The concentrations of the His-tagged protein in the lysate has also been determined and compared with other alternative methods. This method will later be used to analyse protein concentrations during development and optimization of chromatographic purification process.

Surface Plasmon Resonance (SPR) sensors are thin-film refractometers that measure changes in the refractive index that take place at the surface of a metal film supporting a surface plasmon (Homola, 2008). The research activity consisted on a study and realization of innovative Surface Plasmon Resonance based sensors and of their applications, in particular for the environment monitoring. In order to investigate the possibility of creating innovative SPR sensors, computer simulations of optical structures supporting surface plasmon polaritons and comprising peculiar materials were implemented. In particular SPR sensors based on metals showing Inverted Surface Plasmon Resonance and a single layer of Graphene (SGL) were simulated. An article has been submitted on this study. Surface Plasmon Resonance sensor prototypes were also realized in laboratory. By means of a first SPR sensor with dynamic setup, measurements with Helium and Pentane gases were made, then an SPR sensor with a static setup was assembled, refined and as a following improvement in the optical components an adaptive mirror also introduced, which was able to counteract, if present, a lens defocus, spherical aberration, coma and astigmatism . Moreover the elements of a feasible wireless sensor network based on Surface Plasmon Resonance sensors, the possible data that can be inferred from a SPR sensor and a possible data handling strategy were determined along with an evaluation of the sensor module energy requirements. Then two small wireless sensor network test setups were implemented in laboratory, each one composed of two SPR sensors controlled by a computer or a microcontroller, ZigBee antennas and a main computer for the data reception and diffusion into Internet. The feasibility of a Wireless Sensor Network based on SPR sensors, conceived for environmental pollutants detection and with broadband internet connection, has been demonstrated and two different laboratory setups for a test Wireless Sensor Network based on Surface Plasmon Resonance Sensors were realized.
I sensori basati sulla plasmonica di superficie (SPR) sono rifrattometri, basati sulla fisica dei film sottili, che misurano le variazioni di indice di rifrazione che avvengono sulla superficie di uno strato metallico supportante un plasmone di superficie (Homola , 2008). L’ attività di ricerca si è sviluppata come uno studio ed implementazione di sensori SPR innovativi e delle loro possibili applicazioni, in particolare per la rilevazione di sostanze inquinanti. Sono stati simulati in ambiente Matlab sensori SPR innovativi, comprendenti materiali peculiari. Tali sensori comprendono in particolare metalli mostranti una Risonanza Plasmonica Invertita (ISPR), oltre che un singolo strato di Graphene (SGL). Un articolo è stato sottomesso su tali studi. Sono stati inoltre implementati in laboratorio vari prototipi di sensori basati sulla plasmonica di superficie. Innanzi tutto sono state effettuate delle misure di riflettività con i gas elio e pentano mediante un sensore basato sulla plasmonica di superficie e con un setup dinamico, quindi è stato creato un nuovo sensore utilizzante un un sistema ottico di tipo statico ed un prisma cilindrico ad alto indice di rifrazione, migliorando il più possibile la qualità del fascio ottico e filtrandolo opportunamente. Altresì è stato innovativamente utilizzato nel setup ottico uno specchio deformabile, in grado di correggere le aberrazioni ottiche presenti nello stesso. Oltre a ciò sono stati individuati i possibili elementi di una rete wireless di sensori SPR progettata per il monitoraggio ambientale, i dati ottenibili da un sensore SPR, una strategia per la diffusione dei dati ed una stima dei consumi energetici. Infine sono stati implementati in laboratorio due diversi setup di prova per una piccola rete wireless di sensori, formata da due sensori SPR controllati da un computer o da un microcontrollore, antenne ZigBee e da un computer principale per la ricezione, analisi e diffusione in Internet dei dati. L’ attività di ricerca presentata in questa tesi ha quindi dimostrato la possibilità della creazione di una rete wireless di sensori basati sulla Plasmonica di Superficie e con accesso Internet a banda larga, finalizzata alla rilevazione di sostanze inquinanti in ambiente acquoso, e due piccole versioni di prova della stessa sono state implementate in laboratorio.

PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO
COORDENAÇÃO DE APERFEIÇOAMENTO DO PESSOAL DE ENSINO SUPERIOR
PROGRAMA DE SUPORTE À PÓS-GRADUAÇÃO DE INSTS. DE ENSINO
Espectroscopia de ressonância plasmônica de superfície (SPR) é uma técnica óptica amplamente utilizada para monitorizar as alterações físicas ou químicas que ocorrem em uma interface metal - dielétrico. A medição simultânea da espessura e do índice de refração de filmes finos orgânicos, adsorvidos ou depositados sobre a superfície plana de um metal, requer duas medições independentes seguindo uma metodologia designada na literatura como método de duas cores ou método de dois meios. Na primeira, as duas medições são realizadas utilizando diferentes comprimentos de onda da radiação eletromagnética interagindo com a amostra. Na segunda, o índice de refração do meio externo (gás, líquido) é alterado entre as duas medições. Enquanto o primeiro método implica no conhecimento da função de dispersão da fase orgânica, o segundo só produz resultados precisos quando as moléculas orgânicas não interagem quimicamente com o fluido externo. Ambos os métodos apresentam dificuldades quando são aplicados à caracterização de materiais luminescentes orgânicos, os quais são na maior parte do tempo altamente reativos à umidade e ao contato com solventes orgânicos. Neste trabalho foi montado um espectrômetro de SPR automatizado. Primeiramente, ele foi testado na caracterização de amostras feitas no laboratório em termos do valor absoluto, e da homogeneidade das constantes ópticas da deposição metálica que suporta a onda de plasma. Nós demonstramos que medições precisas de constantes ópticas permitem a determinação do índice de refração de filmes finos orgânicos luminescentes, evaporados termicamente utilizando o método de substrato com dois metais. Este método, que até onde sabemos é apenas teorizado na literatura, foi aplicado a uma amostra encapsulada com um filme fino de Alq3 comercial. Além disso, a interface metal/Alq3 foi exposta a ar, e a degradação foi monitorada em tempo real, indicando uma diminuição progressiva do ângulo de ressonância da amostra.
Surface Plasmon Resonance Spectroscopy (SPR) is an optical technique widely used to monitor the physical or chemical changes occurring at a metal-dielectric interface. The simultaneous measurement of the thickness and the index of refraction of organic thin films adsorbed or deposited on the metal flat surface require two independent measurements following a methodology commonly named in literature as Two-Colors Method or Two-Medium Method. In the first one, the two measurements are performed using different wavelength of the electromagnetic radiation interacting with the sample. In the second one the index of refraction of the external medium (gas, liquid) is changed between the two measurements.While the first method implies the knowledge of the dispersion function of the organic layer, the second one gives accurate results only when the organic molecules don t interact chemically with the external fluid. Both of these methods present difficulties when applied to the characterization of luminescent organic materials, most of the time highly reactive to humidity and to the contact with organic solvents. In this work an automated SPR spectrometer was assembled and first tested on the characterization of home-made samples in terms of the absolute value and homogeneity of the optical constants of the metal deposition supporting the plasma wave. We demonstrate that accurate measurements of such optical constants allow the determination of the index of refraction of thermally evaporated luminescent organic thin films using a Two-Metal Substrate Method. This method, to our knowledge only theorized up to now in literature, has been applied to an encapsulated sample containing a thin film of commercial Alq3. Further, the degradation of the metal/Alq3 interface exposed to air has been real time monitored indicating a progressive drop in the angle of resonance of the sample.

Variable pressure electron beam etching and lithography for Teflon AF has been demonstrated. The relation between dose and etching depth is tested under high vacuum and water vapor. High resolution structures as small as 75 nm half-pitch have been resolved. Several simulation tools were tested for surface plasmon excitation. Grating based dual mode surface plasmon excitation has been shown numerically and experimentally.

Nanotechnology has advanced to the point that nanoparticles can now be fabricated in a broad variety of shapes from a wide range of materials, each with their own properties and uses. As the list of manufacturable particles continues to grow, a new frontier presents itself: assembling these existing nanoparticles into more complicated nanoscale structures. The primary objective of this thesis is to demonstrate and characterize one such method of nanoscale construction, the plasmonically directed self-assembly of gold nanospheres onto both silver nanospheroids and gold nanorods. At the heart of this research is a the use of a photocleavable ligand (1-(6-Nitrobenzo[d][1,3]dioxol-5-yl)ethyl(4-(1,2-Dithiolan-3-yl)butyl) carbamate), which is capable of forming a photoreactive self-assembly monolayer (SAM) on gold and silver surfaces. After photoactivation, this SAM becomes positively charged at low pH, allowing it to electrostatically bind with negatively charged gold nanospheres (or other negatively charged nanoparticles). In this thesis, I describe both a secondary photoreaction that this ligand is capable post-photocleavage, which removes the ligand's ability to bind to negatively charged gold nanospheres, allowing for, among other assembly methods, reverse photopatterning. I further show that this photocleavable ligand can be used in conjunction with gold nanospheres to create aligned, metal structures on silver nanospheroid surface by exposure to linearly polarized UV light. Similarly, I also demonstrate how the ligand can be used to preferentially bind gold nanospheres to the ends of gold nanorods with the use of ultrafast femtosecond pulsed 750 nm laser light, making use of multi-photon absorption. Both methods of self-assembly, as well as the secondary photoreaction, are dependent on the plasmonics of the metal nanoparticles. This thesis also goes into the backgrounds of plasmonics, plasmonically mediated catalysis, self-assembly, and photocleavable chemicals.
Ph. D.

A mixed self assembling monolayer (mSAM) chip with attached heparin was developed to analyze heparin-protein interactions using a Reichert Inc, SR7000, surface plasmon resonance (SPR) instrument. The heparin was attached via streptavidin-biotin linkage where the streptavidin was covalently coupled to the mSAM and biotinylated heparin bound to it. These chips were then used to quantify the interactions of fibroblast growth factor-2 (FGF-2) with the surface bound heparin. Kinetic rate constants of association and disassociation were calculated. The association data of FGF-2 with heparin was fit to a single compartment, well-mixed model as the data did not exhibit mass transfer limitations. The results suggested that rebinding was prevalent and observed disassociation rates differed significantly in the presence of competing soluble heparin during disassociation. Our results indicate that the Reichert instrument and mSAM chips can be used to analyze heparin-protein interactions but that a careful protocol, outlined in this thesis, should be followed to obtain optimal data.
Master of Science

The present research focused on the development of a new methodology to assess the strength of the interaction between vaccine antigens and elicited polyclonal antibodies through SPR biosensors. Quantifying the binding strength of polyclonal antibodies is of first importance to evaluate the quality of the vaccine as well as to increase the scientific knowledge of immune protection mechanisms. To now the development of such tool has been complicated by the non-specific binding caused by high protein abundance in the blood and serum samples but also by the way of interpreting the data resulting from multi-interaction events measured at the same time. At first, we unsuccessfully tried to segregate the individual affinity contribution of each antibody population by measuring the signal as the sum of singular interactions. Differentiation of the singular contribution would have needed the fulfillment of the “additivity” hypothesis, meaning that each antibody bind identically alone or in mixture with other antibody. This hypothesis was not met and mathematical assessment by the sum of singular contribution led to fitting results that did not reflect the biological reality. It was therefore decided to switch the analysis method and to measure the end association binding level reached by the different samples injected at the same specific antibody content. The dissociation behavior was interpreted by the percentage of binding after long and fixed dissociation time. In a first application, we compared the antibodies elicited by two different commercially available vaccines and we showed that the binding interaction was not concentration dependent as, highly different levels were reached when injecting identical antibody concentration. No statistical significant difference was observed between both vaccines. Research firstly focused on the decrease of the non-specific binding and we found that ionic strength was a key parameter, increasing the buffer salt concentration reduced the non-specific binding without diminishing the binding strength. The sample composition was also a key parameter and purifying the IgG allowed to decrease dramatically the undesired binding events. A second application aimed at showing the equivalence between two different antigen constructions for two antibodies population. Even if identical antigen level immobilization is a challenge, the methodology is completely suitable to perform a 2-dimensional comparison (ligand and analyte). A last application was dedicated to the comparison between D and Q-pan Flu vaccines, and results showed that there was no statistical evidence of significant differences between both vaccines. End association level correlated well with haemagglutination inhibition assay at least when serum samples were not diluted at the same antibody content. This last application also showed that throughput may be extended to more than 50 samples per 80 hours
Doctorat en Sciences agronomiques et ingénierie biologique
info:eu-repo/semantics/nonPublished

Reliable analytical tools are important for time efficient and economical process development, production and batch release of pharmaceuticals. Therapeutics recovered from human plasma, called plasma protein products, involve a large pharmaceutical industry of plasma fractionation. In plasma fractionation of human immunoglobulin G (hIgG) and albumin (HSA) recommended analysis techniques are regulated by the European Pharmacopoeia and are including total protein concentration assays and zone electrophoresis for protein composition and purity. These techniques are robust, but more efficient techniques with higher resolution, specificity and less hands-on time are available. Surface plasmon resonance is an optical method to study biomolecular interactions label-free in real time. This technology was used in this master thesis to set up assays using Biacore systems for quantification of HSA and hIgG from all steps of chromatographic plasma fractionation as a tool for process development and in-process control. The analyses have simplified mass balance calculations to a high extent as they imply specific detection of the proteins compared with using total protein detection. The assays have a low hands-on time and are very simple to perform and the use of one master calibration curve during a full week decreases analysis time to a minimum. Quick, in-process control quantification of one sample is easily obtained within <10 minutes. For final QC of hIgG or for process development, an assay to quantify the distribution of the IgG subclasses (1-4) was set up on Biacore and showed significantly lower hands-on time compared with a commercial ELISA. All assays showed reliable quantification and identification performed in unattended runs with high precision, accuracy and sensitivity.

The aim of the submitted study is to develop molecular imprinting based surface plasmon resonance (SPR) sensor for real-time silver ion detection. For this purpose polymeric nanofilm layer on the gold SPR chip surface was prepared via UV polymerization of acrylic acid at 395 nm for 30 minutes. N-methacryloyl- L cysteine used as the functional monomer to recognize the silver(I) ions from the aqueous solutions and methylene bisacrylamide used as the crosslinker for obtaining structural rigidity of the formed cavities. Silver(I) solutions with different concentrations were applied to SPR system to investigate the efficiency of the imprinted SPR sensor in real time. For the control experiments, non-imprinted SPR sensor was also prepared as described above without addition of template “silver(I) ions”. Prepared SPR sensors were characterized with atomic force microscopy (AFM). In order to show the selectivity of the silver(I) imprinted SPR sensor, competitive adsorption of Cu(II), Pb(II), Ni(II) ions was investigated. When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/34892

The core of my research activity during the Ph.D. period has been the study and the development of Surface Plasmon Resonance (SPR) based sensors for the detection of molecules of biological and medical interest. In particular, between the different configurations allowing plasmon excitation, I have focused my research on the study of nanostructured gratings, which allow to achieve a higher sensitivity than the prism coupled sensors and to miniaturize the measurement system. First my activity focused on the development of an opto-electronic bench able to detect plasmonic signal and to transduce it into an electric one. The test bench must allow varying independently some parameters that are fundamental for plasmonic excitation, such as the incident angle of laser beam, the azimuthal angle between the scattering plane and the grating vector, and the incident light polarization. The light modulated by the grating is transduced into electrical current through a photodiodes array and then acquired by a parameters analyzer. I have realized a versatile bench in order to perform measurements of both reflectance, analyzing the light reflected from the grating, and transmittance. The use of a motorized rotation stage has automated the measurement and it is controlled by a custom National Instruments LabVIEW software: in this way only few initial steps must be manually performed. I have analyzed three types of gratings: - Gold sinusoidal grating, optimized for reflectance measurements in incident light polarization modulation, exploiting the sensitivity increase due to a non-zero azimuthal angle. This grating has been provided us by LaNN laboratory (Laboratory of research for Nanofabrication and Nanodevices) of National Council of Research (CNR) of Padova. The grating has been manufactured through lithography (by Laser Interference Lithography-LIL) of a photoresist deposited over a glass (or silicon wafer), nanostructure replica and thermal evaporation of the gold plasmonic layer. First I have analyzed the bare grating, and then I have measured bulk with different refractive indexes in order to estimate sensor sensitivity. Then I have measured if the sensor is able to detect biological molecules, first through tests of avidin detection, exploiting avidin-biotin binding, and then through tests of DNA detection, via complementary Peptide Nucleic Acid (PNA) immobilization. - Gold digital grating, that exploits light extraordinary transmission. This grating has been fabricated by LaNN laboratory of CNR of Padova through Electron Beam Lithography (EBL) technique, and it has been designed in order to realize a simple and compact detection system, since the only sensing parameter considered is incident light polarization. Grating ability to detect surface changes of refractive index has been evaluated by a functionalization process with dodecanethiol, that is a molecule composed of a chain of twelve carbon atoms that forms a layer of well- known thickness and refractive index. - Silver trapezoidal grating, developed thanks to the collaboration with the Spin-Off Next Step Engineering, that has involved me in the last months of my Ph.D.. In fact, I have participated in grating fabrication exploiting the industrial facilities of the Spin-Off, which allow producing high quantity of low-cost devices, suitable to be a disposable sensor. The manufacturing process consists of the development of a stamper obtained through interferential lithography, the replica molding of polymeric substrate and the metal layer deposition through sputtering. These gratings have been optimized for transmittance measurements and their response as a function of incident light and azimuthal angles has been analyzed. Measurements of bulk with different refractive indexes, in order to estimate sensor sensitivity, and then of grating functionalized with different lengths alkanethiols have been performed. All experimental data have been compared with simulations results. In fact the behavior of the gratings has been studied through different simulation methods. In particular the digital gold grating has been studied through Finite Element Method (FEM) implemented in COMSOL Multiphysics; the vector model has been applied for both sinusoidal gold gratings and trapezoidal silver ones. The latter grating has been also analyzed through Rigorous Coupled Wave Analysis (RCWA). As already mentioned, during the last period of my Ph.D., I have collaborated with Next Step Engineering to develop an innovative industrial process that allows creating both grating for plasmonic events detection and electronic/microfluidic hybrid devices within a single, well-established, production line. With this process I have manufactured all the custom devices I used for my experimental activity. Moreover, this industrial process is the object of an Italian patent that is now pending and I am one of the inventors. During my PhD I have also developed microfluidic devices through a particular technique of polymer etching, able to create clear-cut profiles without deforming the planar structure, and also through suitable changes of production process adopted by Next Step Engineering, previously mentioned. The former devices have been used with silver gratings for the measurements of bulk with different refractive indexes.
Il tema principale dell’attività di ricerca che ho svolto durante il mio periodo di Dottorato in Scienza e Tecnologia dell’Informazione è stato lo studio e lo sviluppo di sensori basati sull’effetto di risonanza plasmonica per la rilevazione di molecole di interesse medico e biologico. In particolare, tra le varie configurazioni che permettono l’eccitazione plasmonica, mi sono focalizzata sullo studio dei reticoli nanostrutturati, i quali permettono di raggiungere elevate sensibilità, se paragonati ai dispositivi accoppiati con prisma, e di miniaturizzare e integrare il sistema di misura come obiettivo nel lungo periodo. Inizialmente la mia attività si è concentrata sullo sviluppo di un banco opto-elettronico che permettesse di rilevare il segnale plasmonico e trasdurlo in un segnale elettrico. Il banco doveva essere in grado di variare indipendentemente alcuni parametri determinanti per l’eccitazione plasmonica, ossia l’angolo di incidenza del fascio laser, l’angolo azimutale tra il piano di scattering e il vettore del reticolo, e la polarizzazione della luce incidente. La luce modulata dal reticolo viene poi trasformata in corrente elettrica attraverso un array di fotodiodi, e quindi acquisita attraverso un analizzatore di parametri. Ho mirato a realizzare un banco molto versatile in modo da poter effettuare misure sia di riflettanza, andando ad analizzare la luce riflessa dal reticolo, sia di trasmittanza, analizzando la luce trasmessa dal campione. L’introduzione di uno stadio motorizzato ha permesso di rendere la misura più automatizzata e gestibile via software, attraverso un programma custom sviluppato in LabVIEW, e lasciando manuali solo pochi passaggi iniziali. Ho analizzato tre tipologie diverse di reticoli: - Reticolo d’oro con superficie sinusoidale, ottimizzato per effettuare misure in riflessione con modulazione della polarizzazione della luce incidente, sfruttando l’aumento di sensibilità derivante dall’angolo azimutale non nullo. Tale reticolo è stato fornito dal laboratorio LaNN (Laboratorio di ricerca per la Nanofabbricazione e i Nanodispositivi) del Consiglio Nazionale delle Ricerche (CNR) di Padova. Il reticolo è stato realizzato attraverso litografia interferenziale di uno strato di fotoresist deposto su un vetrino (o silicio), da cui è stato ricavato uno stampo che permette la replica della nano struttura; infine, attraverso un’evaporazione termica, è stato depositato uno strato d’oro. Inizialmente ho analizzato il reticolo in condizione “fresh”; successivamente ho effettuato misure di “bulk” con indici di rifrazione diversi, per poter stimare la sensibilità del sensore. Ho poi misurato la capacità del dispositivo nel rilevare molecole di interesse biologico, dapprima attraverso prove di rilevazione di avidina presente in una soluzione, sfruttando il legame avidina-biotina, poi con prove di rilevazione di singole catene di DNA, attraverso l’immobilizzazione sulla superficie della nanostruttra di acido peptidonucleico (PNA) complementare. - Reticolo d’oro digitale, ideato per sfruttare il fenomeno di trasmissione straordinaria della luce. Tale reticolo è stato realizzato dal laboratorio LaNN del CNR di Padova attraverso la tecnica di litografia a fascio di elettroni (Electron Beam Lithography-EBL) e nasce con l’obiettivo di creare un sistema di rilevazione estremamente semplice, poiché l’unico parametro di sensing, e quindi variabile, è la polarizzazione della luce incidente. La capacità del sistema di discriminare variazioni superficiali di indice di rifrazione è stata valutata funzionalizzando il reticolo con dodecanethiol, ossia una molecola composta da una catena di dodici atomi di carbonio in grado di formare uno strato di dimensioni e indice di rifrazione noti. - Reticolo trapezoidale in argento, nato dalla collaborazione con lo Spin-Off Next Step Engineering, che mi ha coinvolta nell’ultimo periodo di dottorato. Infatti, ho partecipato in prima persona alla realizzazione del sensore, sfruttando le facilities industriali a cui l’azienda ha accesso, permettendo di produrre dispositivi a basso costo e in elevate quantità, quindi adatti ad un utilizzo di tipo “usa e getta”. Il processo di fabbricazione prevede la realizzazione di uno stampo attraverso litografia interferenziale, una fase di replica a stampo su substrato polimerico e la deposizione di uno strato metallico per polverizzazione catodica. Tali sensori sono stati ottimizzati per la misura della luce trasmessa e si è analizzato il comportamento al variare dell’angolo di incidenza e dell’angolo azimutale. Si è quindi misurato il comportamento del sensore in presenza di bulk ad indici di rifrazione diversi per la stima della sensibilità, e successivamente si sono effettuate misure funzionalizzando il campione con alcantioli di diversa lunghezza. I risultati sperimentali sono stati confrontati con quelli ottenuti dalle simulazioni. Infatti si è studiato il comportamento di ogni reticolo attraverso metodi di simulazione diversi. In particolare il reticolo digitale in oro è stato studiato attraverso il metodo degli elementi finiti (FEM) implementato in COMSOL Multiphysics, il modello vettoriale è stato applicato sia per lo studio del reticolo sinusoidale in oro che del reticolo trapezoidale in argento. Quest’ultimo reticolo è stato analizzato anche attraverso il metodo RCWA (Rigorous Coupled Wave Analysis). Come già accennato, durante l’ultimo periodo di dottorato ho contribuito a sviluppare, in collaborazione con lo Spin-Off dell’università di Padova Next Step Engineering, un innovativo processo di produzione industriale che consente di creare non solo reticoli per la rilevazione di segnali plasmonici, ma anche dispositivi ibridi elettronici/microfluidici per applicazioni biologiche e mediche, all’interno di una singola linea produttiva automatizzata. Con questo processo ho prodotto i reticoli in argento, che ho utilizzato per la mia attività sperimentale. Il processo di produzione è oggetto di un brevetto italiano attualmente in fase di deposito, di cui sono uno degli inventori. Durante il dottorato ho approfondito anche lo sviluppo di dispositivi microfluidici sia attraverso tecniche di incisione polimerica, in grado di creare profili di taglio netti senza deformarne la struttura planare, sia apportando le appropriate modifiche al processo produttivo utilizzato da Next Step Engineering, precedentemente citato. I dispositivi realizzati sono stati utilizzati per le misure di bulk a diversi indici di rifrazione utilizzando i reticoli in argento.

IgM monoclonal gammopathy is a common age-related demyelinating sensory and motor polyneuropathy. It has been shown to be associated with antibodies against myelin-associated glycoproteins (MAG/SGPG). The HNK-1 carbohydrate epitope is a terminal 3-sulfo-glucuronyl residue attached to lactosamine structures and it is shared both in MAG and SGPG (SO4-3-GlcA(β1-3)Gal-(β1-4)GlcNAc(β1-3)Gal-(β1-4)Glcβ(1-1′)Cer). It is mostly expressed in the nervous system and plays an important role in preferential motor reinnervation. Nevertheless, the HNK-1 epitope is difficult to be isolated and synthesized and diagnostic assays used in the clinics are not always reproducible and reliable. Therefore in our study, our goal is to identify a simple synthetic diagnostic tool (peptide or monosaccharide), mimetic of the HNK-1 epitope, able to recognize antibodies in neurogammopathies sera by Surface Plasmon Resonance to be used in earlier stage patients and possibly to monitor disease activity. For this reason, we firstly tried to synthesize this trisaccharide and then we achieved the synthesis of its terminal monosaccharides with different function groups (octyl glucopyranoside, octyl glucuronic acid, octyl 3-O-sulfo-glucuronic acid and 8-amino octyl 3-O-sulfo-glucuronic acid). Then 10 linear and cyclic peptides conformationally and/or structurally mimicking HNK-1 were also synthesized (LSETTI, LSETTl, cyclo(-TTILSE-), cyclo(-TTlLSE-), cyclo(-TKTlLSE-), cyclo(-TETKlLSE-), TYTKlLSE, TY(SO3)TKlLSE, cyclo(-TYTKlLSE-) and cyclo(-TY(SO3)TKlLSE-)). The SPR kinetic binding affinities of all these sugar and peptide mimics were studied with commercial anti HNK-1 antibody using Biacore. Moreover, mimics with highest binding affinities were chosen for antigen-antibody interaction study in IgM gammopathy patients' serum.

The effect of temperature increase on the optical excitation of Surface Plasmon Resonance (SPR) at an Ag-Si metal-semiconductor (M-S) junction at a wavelength of 1 . 1 52 pm is investigated theoretically using computer modeling in Fortran. In order to accurately quantify the SPR, the temperature dependent optical constants for Ag and Si are obtained theoretically or semiempirically , using a Drude model for Ag and previous experimentally determined equations for Si (the behavior of the optical constants for crystalline Si and doped Si are found to have very little deviation between each other for our case). An improvement in the theoretical derivation for the optical constants of Ag is obtained, maintaining self-consistency. The optical constants are utilized to quantify the reflectance of an incident wave on an M-S junction, using Fresnel equations for a four layer system. The reflectivity of the M-S junction is indicative of the surface plasmon generation. There exists much industrial interest in increasing the amount of photocurrent generation in semiconductors for a given number of incident photons. This increase in photocurrent is often referred to as enhancing the quantum efficiency (Q). It has been previously shown by many groups that there can be an appreciable enhancement of Q due to the optical excitation of surface plasmons on a Schottky barrier junction (M-S junction), although all these previous studies were done at room temperature. Hence, the studies of temperature effect of SPR at the M-S junction could lead to interesting effects for the Q as well. In this thesis, we have studied qualitatively the effect of temperature increase on the optical excitation of SPR at an Ag-Si junction. From these results we have attempted to draw inference to the possibility of the enhancement of Q at elevated temperatures for such a diode junction.

Surface plasmon resonance (SPR) active nanohole array substrates offer a diverse biosensing platform with high sensitivity and unique characteristics. This dissertation investigates the sensitivity and fundamental SP features of various nanohole array substrates and demonstrates higher sensitivity than conventional continuous gold platforms, tunability to specific analytes, and great enhancement of the local field intensity. Novel instrumentation and analytical techniques are developed and utilized to assess the nanohole array SPR sensing substrates in the near infrared as well as with interaction of other nanostructures.

The nanohole array substrates are evaluated throughout the near-infrared (NIR) region by novel SPR instrumentation and methodology that extends the working SPR wavelength range and measurement reliability. Development of a robust NIR-SPR instrument allows access to higher wavelength ranges where sensitivity is improved and novel SP modes and plasmonic materials may be investigated. Different aspects of the NIR-SPR instrument, including temporal stability, mechanical resilience and sensitivity, are evaluated and presented. Furthermore, a method is developed for improving precision and accuracy of empirically determined SP penetration depth, a merit of SPR spectroscopy sensitivity. The technique incorporates an adsorbate-metal bonding effect which improves the consistency in the penetration depth value calculated at different adsorbate thicknesses from 41-1089% relative deviation (without bonding effect) to 2-11% relative deviation (with bonding effect). It also improves the experimental agreement with theory, increases the accuracy of assessing novel plasmonic materials and nanostructures, and increases the precision in adsorbate parameters calculated from the penetration depth value, such as thickness, binding affinity, and surface coverage.

Utilizing this NIR-SPR instrument and improved technique for calculation of penetration depth, the sensitivity and various SP modes of the nanohole arrays throughout the NIR range are evaluated, and an improvement in sensitivity compared to conventional continuous gold is observed. Both the Bragg SPs arising from diffraction by the periodic holes and the traditional propagating SPs are characterized with emphasis on sensing capability of the propagating SPs. There are numerous studies on the transmission spectroscopy of nanohole arrays; however this dissertation presents one of the few studies in Kretschmann mode, and the first in the near infrared, where greater surface sensitivity is observed. The sensitivity profile of various nanohole array parameters (periodicity, diameter, excitation wavelength) and SP modes is also presented.

Further control and enhancement of the SP field is pursued by interaction between nanohole array substrate and nanoparticles to exploit field intensification between plasmonic structures, i.e. gap mode enhancement. Under specific conditions, the SPs couple together and the electric field between the structures is amplified and localized, which may be exploited for sensing purposes and surface enhanced techniques, including tip enhanced Raman spectroscopy (TERS) or surface enhanced Raman spectroscopy (SERS). A technique for observing nanohole array-nanoparticle distance dependent SP interaction is developed and utilized to demonstrate SP interaction. Scanning probe microscopy controls the position of a single nanoparticle (SNP) affixed to an atomic force microscope probe, and the location specific interaction of the SNP-nanohole array surface plasmons is measured by darkfield surface plasmon resonance spectroscopy. Coupling of the nanoparticle to the nanohole array exhibits a maximum when the SNP resides within a nanohole, which resulted in a maximum SPR wavelength shift of 17 nm and an increase in scatter intensity. This dissertation presents the first empirical observations of SPM controlled gap mode enhancement of more complex nanostructures and allows for optimization of positioning prior to use in sensing.

The study and understanding of molecular interactions is fundamentally important in today's field of life sciences and there is a demand for well designed surfaces for biosensor applications. The biosensor has to be able to detect specific molecular interactions, while non-specific binding of other substances to the sensor surface should be kept to a minimum.                                                                                                                                                                                The objective of this master´s thesis was to design sensor surfaces based on self-assembled monolayers (SAMs) and evaluate their structural characteristics as well as their performance in Biacore systems. By mixing different oligo (ethylene glycol) terminated thiol compounds in the SAMs, the density of functional groups for bimolecular attachment could be controlled.  Structural characteristics of the SAMs were studied using Ellipsometry, Contact Angle Goniometry, IRAS and XPS. Surfaces showing promising results were examined further with Surface Plasmon Resonance in Biacore instruments.

Mixed SAM surfaces with a tailored degree of functional COOH groups could be prepared. The surfaces showed promising characteristics in terms of stability, immobilization capacity of biomolecules, non-specific binding and kinetic assay performance, while further work needs to be dedicated to the improvement of their storage stability. In conclusion, the SAM based sensor surfaces studied in this thesis are interesting candidates for Biacore applications.

Dans un avenir proche, les dispositifs de détection médicaux miniaturisés en temps réels (lab-on-chip) seront au centre de la révolution des méthodes de diagnostics médicaux et d’identification des processus biologiques et cela, autant au niveau clinique qu’au niveau de la recherche. Pour y arriver, il est important de développer des chimies de surface stables et spécifiques, ce qui demande une compréhension des interactions intermoléculaires à l’interface liquide/solide. Pour bien comprendre ces interactions, il est important de développer des instruments adaptés à la mesure près de l’interface liquide/solide des différentes caractéristiques à identifier. Ce projet de recherche présente la conception, la fabrication et les expériences tests d’un capteur multimodal pour l’identification de processus biologiques à l’interface basés sur des technologies de résonance des plasmons de surface (SPR) et de microcalorimérie. Ces deux technologies mises ensemble vont permettre d’effectuer des mesures de la cinétique des interactions ainsi que des caractéristiques thermodynamiques. En premier lieu, les caractéristiques d’une interaction intermoléculaire à l’interface d’une réaction d’hybridation d’ADN furent définies afin d’en déduire un cahier des charges pour les transducteurs. Suite à cela, la conception des transducteurs microcalorimétrique et SPR furent réalisés en tenant compte des contraintes de chacun des transducteurs. Suite à la conception théorique des différentes parties du capteur, un procédé de fabrication compatible avec les méthodes de fabrication standard de la microélectronique fut défini et testé. Afin de s’assurer de la fonctionnalité des dispositifs ainsi fabriqués, des tests de fonctionnalisation de surface furent appliqués sur les échantillons afin de tester la compatibilité du procédé de fonctionnalisation avec les méthodes de fabrication et avec une chimie de surface type. Pour terminer, un système de mélange actif fut testé et caractérisé avec le dispositif de microcalorimétrie afin de s’assurer qu’il était possible de mélanger les fluides avec les produits biologiques pour s’assurer de la qualité de la réaction de surface. Le système développé pourra être utilisé pour effectuer la mesure d’hybridation d’ADN à l’interface. Le système intègre deux modalités permettant la caractérisation en temps réel des interactions intermoléculaires à l’interface liquide/solide. Ce type de système permet la mesure de la cinétique de différents modèles biologiques tels que les puces à sucre encore certains récepteurs cellulaires ou la mesure de conformation moléculaire à l’interface. Des mesures d’oxydation du glucose catalysée par la glucose oxydase sont montrées
To begin with, the characteristics of a DNA hybridization intermolecular interaction at the interface were defined in order to deduce the specifications for our transducers. Following this, the SPR and microcalorimetric transducer will be design by taking into account the constraints of each one. Following the theoretical design of the sensor, a manufacturing process compatible with standard methods of microelectronics manufacturing was tested and identified. To ensure the functionality of the devices, a test of surface functionalization on the sensor was applied to test the compatibility of the manufacturing process with the surface functionalization methods. Finally, a system of active mixing was tested and characterized with a microcalorimetric device to ensure it was possible to mix fluids with organic products to be sure of the quality of the surface reaction. The system developed can be used to mesure DNA hybridization at the interface. This system incorporates two modalities for real-time characterization of intermolecular interactions near the solid/liquid interface. This type of system allows the kinetic measurement of different biological models such as cellular receptors or it is possible to have some molecular measure conformation near the interface. Oxidation of glucose with the enzyme glucose oxidase was shown to present the possibility to measure a biological interaction

Proliferating cell nuclear antigen (PCNA) is an essential protein in the cell. It is involved in transcription and many types of DNA repair and replication. Homologues of this protein are found in all orders of life. The high level of conservation and essential nature of PCNA infers that it may be a potential drug target for anti-caner drugs in humans and also a potential anti-parasitic target. X-ray structures of PCNA from Homo sapiens (Hs), Schizosaccharomyces pombe (Sp) and Leishmania major (Lm) are now available and can be used as a template for structure based drug design. In this work PCNA from these three species have been prepared in milligram quantities for biochemical and biophysical studies. The previously unknown structure of LmPCNA has been solved in an uncomplexed form and also complexed with a dodecapeptide to a resolution of 3.0Å. A comparison of PCNA structures and their peptide complexes for the three species identifies structural differences which may be relevant in analysing thermodynamic contributions of binding. All eukaryotic PCNA molecules exist as ring shaped trimers which form around DNA. In this work the oligomeric state of LmPCNA has been determined to be hexameric both in solution and in the crystal. It has also been hypothesised that HsPCNA is hexameric however these would seem to form hexamers in which the trimeric rings associate “back-to-back” while LmPCNA trimers would seem to associate “face-to-face”. The binding affinities for these three PCNAs have been determined with a selection of peptides derived from the Hs p21 protein. This work has shown, using a selection of different techniques including Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry (ITC) and Dynamic Scanning Fluorimetry (DSF); that HsPCNA and SpPCNA have similar affinities for a 12mer peptide (Kd of ~1μM) however LmPCNA shows significantly weaker interactions (Kd of ~10μM). This is most likely due to divergence in the sequence and structure of LmPCNA. A systematic investigation by SPR on the effect of peptide linker length on binding has been carried out using a series of synthesised peptides with different lengths of chemical spacer. The series of streptavidin immobilised peptides show that longer spacers are required for the recovery of the PCNA peptide binding affinity. The results presented in this work indicate that a linker length of at least 20Å is required for measurable protein binding activity. This interaction is improved with longer peptide spacers.

Cette thèse présente la conception et la mise en œuvre d'un imageur CMOS pour être utilisé dans biocapteurs intégrés basés sur Résonance Plasmonique de Surface (SPR). Tout d'abord, les conditions optimales pour la résonance plasmon dans une interface compatible CMOS / post-CMOS sont obtenus par modélisation avec COMSOL. Deuxièmement, un imageur CMOS de Colonne Actif (CMOS-ACS) du 32x32 pixels est mis en œuvre sur une technologie CMOS 0,35 um. Dans une interface d'or-eau avec une excitation de prisme, on constate que pour les prismes avec des indices de réfraction de 1,55 et 1,46, le couplage optimal avec le plasmon est obtenu pour des films d'or d'une épaisseur de 50 et 45 nm, respectivement. Dans ces conditions, environ 99,19% et 99,99% de l'énergie de la lumière incidente est transférée à le surface plasmon pour les deux prismes respectivement, à condition que la lumière incidente, avec une longueur d'onde de 633 nm, arrive avec un angle d'incidence de 68,45° et 79,05° respectivement. Il est également obtenu qu'un changement de RIU 10-4 de l'indice de réfraction du milieu diélectrique, produit un changement de 0,01 ° dans l'angle de résonance de plasmons qui, dans un schéma de modulation d'intensité de lumière produit une variation de 0,08% dans la lumière réfléchie au photodétecteur. En ce qui concerne le imageur CMOS, une photodiode n-well/p-substrate est choisi comme l'élément de photodétection, en raison de sa faible capacité de jonction, ce qui conduit à un rendement élevé et le gain de conversion élevé comparativement à une photodiode n-diff/p-substrate. Des simulations sur ordinateur avec Cadence et Silvaco produit une capacité de jonction de 31 FF et 135 fF respectivement. Le pixel de l'imageur est basé sur une configuration à trois transistors (3T) et présente un facteur de remplissage de 61%. Le circuit de lecture utilise une technique de capteur de colonne actif (ACS) pour réduire le bruit à motif fixe (Fixed Pattern Noise ou FPN en anglais) liée au le Capteur à Pixels Actif (APS) traditionnelle. En outre, Non-Corrélés Echantillonnage Double (Non-Correlated Double Sampling ou NCDS en anglais) et Delta double échantillonnage (DDS) sont utilisés comme techniques de réduction du bruit. Un montage optique expérimental est utilisé pour caractériser les performances de l'imageur, et nous avons obtenu un gain en conversion de 7,3 uV/e-, une capacité de jonction de la photodiode de 22 fF, un bruit de lecture de 324,5 uV, ce qui équivaut à 45 électrons, et une gamme dynamique de 50,5 dB. Les avantages de l'ACS et NCDS-DDS sont observées dans le niveau faible de FPN du pixel et de la colonne, avec une valeur de 0,09% et 0,06% respectivement. Le travail présenté dans cette thèse est une première étape vers l'objectif de développer une plateforme entièrement intégrée SPR pour biocapteurs, incorporant source de lumière, l'interface SPR, canal microfluidique, les éléments d'optique et imageur CMOS
This dissertation presents the design and implementation of a CMOS imager for use in integrated biosensors based on Surface Plasmon Resonance. First, the optimal conditions for plasmon resonance in a CMOS/Post-CMOS compatible interface are obtained by COMSOL modelling. Second, a 32x32-pixel CMOS-Active Column Sensor (CMOS-ACS) is implemented on 0.35 um CMOS technology. In a gold-water interface with prism excitation, it is found that for prisms showing refractive indexes of 1.55 and 1.46, optimal plasmon coupling is obtained for gold films with thicknesses of 50 and 45 nm respectively. Under these conditions, approximately 99.19% and 99.99% of the incident light's energy is transferred to the surface plasmon for both prism respectively, provided that the incident light, with a wavelength of 633 nm, arrives with incidence angles of 68.45° and 79.05° respectively. It is also obtained that a change of 10-4 RIU in the refractive index of the dielectric medium, produces a change of 0.01° in the plasmon resonance angle, which under a light intensity modulation scheme produces a change of 0.08% in the reflected light's energy reaching the photodetector. Concerning the CMOS imager, a n-well/p-substrate photodiode is selected as the photosensing element, due to its low junction capacitance, which results in high efficiency and high conversion gain compared to the n-diff/p-substrate photodiode. Computer simulations with Cadence and Silvaco produced a junction capacitance of 31 fF and 135 fF respectively. The imager's pixel is based on a three-transistor (3T) configuration and shows a fill factor of 61%. The readout circuitry employs an Active Column Sensor (ACS) technique to reduce the Fixed Pattern Noise (FPN) associated with traditional Active Pixel Sensors (APS). Additionally, Non-Correlated Double Sampling (NCDS) and Delta Double Sampling (DDS) are used as noise reduction techniques. An experimental optical setup is used to characterize the performance of the imager, obtaining a conversion gain of 7.3 uV/e-, a photodiode junction capacitance of 21.9 fF, a read noise of 324.5 uV, equivalent to ~45 e- and a dynamic range of 50.5 dB. The benefits of ACS and NCDS-DDS are observed in the low pixel and column FPN of 0.09% and 0.06% respectively. The work presented in this thesis is a first step towards the goal of developing a fully integrated SPR-biosensing platform incorporating light source, SPR interface, microfluidic channel, optical elements and CMOS imager

Identification of pathogens living in biofilms of chronic infections has been difficult with PCR, serological, biochemical and culture techniques. The study aims at the detection of bacterial pathogens in biofilms of biological secretions using SPR analysis Biacore. The antibodies were developed by isolating mononuclear lymphocytes from the blood of the patients who sustained systemic infection. The isolated lymphocytes had antibody secreting B cells (plasma cells) which were identified using flow cytometry analysis. The antibodies produced (n=4) were used to immobilize CM5 chip of Biacore to detect the bacteria in ulcer secretions with wound secretions of healthy volunteers as controls. The results from Surface Plasmon Resonance (SPR) analysis and culture technique were compared and statistically there was no significant difference obtained. The results from present study suggest that SPR analysis could be used as an alternative system for detection of bacteria in poly-microbial samples and detect the organisms that might not be discovered by culture or PCR method.

Ligandgesteuerte Ionenkanäle sind Membranproteine, die an der Weiterleitung von Reizen und an der Kommunikation zwischen Zellen beteiligt sind. Große Bedeutung besitzt die Messung der Aktivierung der Ionenkanäle beispielsweise in der Medizin (z.B. Ionenkanalerkrankungen), der Pharmazie (z.B. Medikamenten-Screening) und in der Bionanotechnologie (z.B. molekulare Schalter). In all diesen Gebieten besteht die Forderung nach hohen Probendurchsätzen bei sehr hohem Informationsgehalt. Etablierte elektrochemische Detektionsmethoden erfüllen diese Forderung nicht. Um dieses Defizit zu überwinden, wurde ein Ionenkanalsensor-Array mit optischer, paralleler Detektion entwickelt. Eine mikrostrukturierte Polymethyl(meth)acrylat (PMMA)-Schicht dient als Grundgerüst des Arrays. Über die Mikroporen, die nur wenige Mikrometer Durchmesser aufweisen, wird eine Lipidmembran gespannt, in die Ionenkanäle eingebaut werden. Wird der Ionenkanal aktiviert, strömen Ionen in die Mikroporen und führen zu einer messbaren Veränderung des Brechungsindexes. Mittels Oberflächenplasmonen-Resonanz Imaging lässt sich die Aktivierung der Ionenkanäle markierungsfrei und direkt bestimmen. Stabile, die Mikrostruktur überspannende Lipidmembranen wurden durch eine neu entwickelte Stempeltechnik und durch eine Oberflächenmodifikation der PMMA-Mikrostruktur erzielt. Für die Charakterisierung und den Funktionsnachweis des Sensoraufbaus wurden das infrarot-spektroskopische Imaging und die Fluoreszenzmikroskopie eingesetzt. Schließlich konnte gezeigt werden, dass eine Verbesserung der Empfindlichkeit durch das lokale Aufkonzentrieren der durch den Ionenkanal geströmten Metallionen am Porengrund mit oberflächengebundener 2-(Benzylsulfid)-18-Krone-6 möglich ist.

Wood is a complex biocomposite that exhibits a high work of fracture, making it an ideal model for multiphase man-made materials. Typically, man-made composites demonstrate interfacial fracture at failure due to abrupt transitions between neighboring phases. This phenomenon does not occur in wood because gradual phase transitions exist between regions of cellulose, hemicellulose, and lignin and therefore adhesion between adjacent phases is increased. The formation of interphases occurs as a consequence of the self-assembly process which governs the formation of wood. If this process was understood more thoroughly, perhaps tougher man-made, biobased composites could be prepared. To study self-assembly phenomena in wood, a system composed of a model copolymer (pullulan abietate, DS=0.027) representing the lignin-carbohydrate complex (LCC) and a model surface for cellulose fibers was used. The self-assembly of the polysaccharide pullulan abietate (DS=0.027) onto a regenerated cellulose surface prepared using the Langmuir-Blodgett (LB) technique was studied via surface plasmon resonance (SPR). Rapid, spontaneous, and desorption-resistant cellulose surface modification resulted when exposed to the model LCC. Adsorption was quantified using the de Feijter equation revealing that between 9-10 anhydroglucose units (AGUs) adsorb per nm&178; of cellulose surface area when cellulose is exposed to pullulan abietate (DS=0.027) compared to the adsorption of 6.6 AGUs per nm&178; of cellulose surface area when cellulose is exposed to unsubstituted pullulan.
Master of Science

The three different platform candidates were antibody microarray, surface Plasmon resonance (SPR) and bead array. Another objective of this project was to explore other applications of these platforms, and the selected example application was to explore other applications of these platforms for hybridoma screening. Since antibodies against plant pathogens have previously been produced, characterized and used in development of the three different platforms, to examine the possibility of applying the platforms to facilitate the screening of hybrid om a, pilhogenic foodbome bacterium Listeria monocytogenes was used as a model study. In summary, antibody array and bead array technologies were demonstrated to be able to detect multiple plant pathogens at the same time. Both were shown to be able to detect the pathogens in the real samples from fields. making them good candidates for plant industries. On the other hand, despite considerable effort to incr¢ase the sensiritivity of SPR, lower limit of detection could not be achieved. This courd be an intrinsic limitation of this method for detecting a whole cell where the size of the analytic is bigger than usual SPR analytes such as small compounds. From these technologies. an antibody array was selected for hybridoma screening and was shown to be effective, albeit with lower sensitivity compared to ELISA. The antibody array proved to be a faster and simpler method to screen hundreds of hybricioma 3 clones. A comnbination of biosensor tcchnology ensures good quality screening for hybridoma clones as demonstrated in this study.

Plasmonics techniques, such as surface plasmon resonance (SPR) and surface-enhanced Raman scattering (SERS), have been widely used for chemical and biochemical sensing applications. One approach to excite surface plasmons is through the coupling of light into metallic grating nanostructures. Those grating nanostructures can be fabricated using state-of-the-art nanofabrication methods. Laser interference lithography (LIL) is one of those methods that allow the rapid fabrication of nanostructures with a high-throughput. In this thesis, LIL was combined with other microfabrication techniques, such as photolithography and template stripping, to fabricate different types of plasmonic sensors. Firstly, template stripping was applied to transfer LIL-fabricated patterns of one-dimensional nanogratings onto planar supports (e.g., glass slides and plane-cut optical fiber tips). A thin adhesive layer of epoxy resin was used to facilitate the transfer. The UV-Vis spectroscopic response of the nanogratings supported on glass slides demonstrated a strong dependency on the polarization of the incident light. The bulk refractive index sensitivities of the glass-supported nanogratings were dependent on the type of metal (Ag or Au) and the thickness of the metal film. The described methodology provided an efficient low-cost fabrication alternative to produce metallic nanostructures for plasmonic chemical sensing applications. Secondly, we demonstrated a versatile procedure (LIL either alone or combined with traditional laser photolithography) to prepare both large area (i.e. one inch2) and microarrays (μarrays) of metallic gratings structures capable of supporting SPR excitation (and SERS). The fabrication procedure was simple, high-throughput, and reproducible, with less than 5 % array-to-array variations in geometrical properties. The nanostructured gold μarrays were integrated on a chip for SERS detection of ppm-level of 8-quinolinol, an emerging water-borne pharmaceutical contaminant. Lastly, the LIL-fabricated large area nanogratings have been applied for SERS detection of the mixtures of quinolone antibiotics, enrofloxacin, an approved veterinary antibiotic, and one of its active metabolite, ciprofloxacin. The quantification of these analytes (enrofloxacin and ciprofloxacin) in aqueous mixtures were achieved by employing chemometric analysis. The limit of quantification of the method described in this work is in the ppm-level, with <10 % SERS spatial variation. Isotope-edited internal calibration method was attempted to improve the accuracy and reproducibility of the SERS methodology.
Graduate
2018-02-17

Les besoins actuels grandissants pour l'analyse des interactions biomoléculaires nécessitent le développement de systèmes automatisés à forte capacité et haut débit comme la microscopie de fluorescence qui reste une méthode de prédilection. Bien que les méthodes directes (sans marquage des molécules à analyser) présentent une sensibilité plus faible que celles utilisant des marqueurs, leurs nombreux avantages (suivi en temps réel, préparation simplifiée des échantillons) sont des atouts d'importance pour l'analyse quantitative des interactions biomoléculaires. En outre, l'imagerie en résonance des plasmons de surface permet de mesurer simultanément de nombreuses interactions comme les méthodes avec marqueurs. Pour élaborer un tel dispositif, nous avons d'abord identifié les différents paramètres critiques, susceptibles d'être améliorés, comme la nature de la couche métallique. L'utilisation du capteur ainsi développé repose en grande partie sur la chimie de surface: nous avons choisi la synthèse électrochimique de films de polypyrrole qui permet, de manière contrôlée et structurée, une fonctionnalisation simple et robuste de plots contenant diverses molécules. Parallèlement, nous avons développé un programme d'acquisition d'images dont le traitement permet de suivre en temps réel les réactions biomoléculaires sur chaque plot et d'en extraire constantes d'association, de dissociation et d'affinité entre molécules. Enfin, nous avons démontré les possibilités d'application de ce système à l'étude de maladies héréditaires ou du cancer à travers des interactions ADN/ADN (K-ras), ADN/protéines (p53), protéines/protéines (hCG) et oligosaccharides/protéines (HP6/SDF-1).

Résumé : Malgré le nombre croissant de capteurs dans les domaines de la chimie et la biologie, il reste encore à étudier en profondeur la complexité des interactions entre les différentes molécules présentes lors d’une détection à l’interface solide-liquide. Dans ce cadre, il est de tout intérêt de croiser différentes méthodes de détection afin d’obtenir des informations complémentaires. Le principal objectif de cette étude est de dimensionner, fabriquer et caractériser un détecteur optique intégré sur verre basé sur la résonance plasmonique de surface, destiné à terme à être combiné avec d’autres techniques de détection, dont un microcalorimètre. La résonance plasmonique de surface est une technique reconnue pour sa sensibilité adaptée à la détection de surface, qui a l’avantage d’être sans marquage et permet de fournir un suivi en temps réel de la cinétique d’une réaction. L’avantage principal de ce capteur est qu’il a été dimensionné pour une large gamme d’indice de réfraction de l’analyte, allant de 1,33 à 1,48. Ces valeurs correspondent à la plupart des entités biologiques associées à leurs couches d’accroche dont les matrices de polymères, présentés dans ce travail. Étant donné que beaucoup d’études biologiques nécessitent la comparaison de la mesure à une référence ou à une autre mesure, le second objectif du projet est d’étudier le potentiel du système SPR intégré sur verre pour la détection multi-analyte. Les trois premiers chapitres se concentrent sur l’objectif principal du projet. Le dimensionnement du dispositif est ainsi présenté, basé sur deux modélisations différentes, associées à plusieurs outils de calcul analytique et numérique. La première modélisation, basée sur l’approximation des interactions faibles, permet d’obtenir la plupart des informations nécessaires au dimensionnement du dispositif. La seconde modélisation, sans approximation, permet de valider le premier modèle approché et de compléter et affiner le dimensionnement. Le procédé de fabrication de la puce optique sur verre est ensuite décrit, ainsi que les instruments et protocoles de caractérisation. Un dispositif est obtenu présentant des sensibilités volumiques entre 1000 nm/RIU et 6000 nm/RIU suivant l’indice de réfraction de l’analyte. L’intégration 3D du guide grâce à son enterrage sélectif dans le verre confère au dispositif une grande compacité, le rendant adapté à la cointégration avec un microcalorimètre en particulier. Le dernier chapitre de la thèse présente l’étude de plusieurs techniques de multiplexage spectral adaptées à un système SPR intégré, exploitant en particulier la technologie sur verre. L’objectif est de fournir au moins deux détections simultanées. Dans ce cadre, plusieurs solutions sont proposées et les dispositifs associés sont dimensionnés, fabriqués et testés.
Abstract : In spite of the growing number of available biosensors, many biochemical reactions and biological components have not yet been studied in detail. Among them, some require the combination of several detection techniques in order to retrieve enough information to characterize them fully. An unknown reaction based, for example, on DNA hybridization could be characterized with an electrochemical sensor, a mechanical sensor and an optical sensor, each giving a different type of information. The main objective of the work presented here is to design, fabricate and characterize a flexible integrated optical biosensor based on surface plasmon resonance, intended to be then combined with other detection techniques, and in particular, a microcalorimeter. Surface Plasmon Resonance (SPR) is well known to be a sensitive technique for surface-based biochemical detection. It has the advantage to be an unlabeled method and provides real time information on the kinetics of a reaction. The flexibility of the proposed SPR biosensor comes from the fact that it is designed for a large range of analyte refractive indices, from 1.33 to 1.48. These values are suitable for most biological entities and their ligand layers, and especially for hydrophilic polymer matrices used to trap DNA or protein entities and introduced in this work. As several biochemical studies require the simultaneous comparison of measurements to a reference or to another measurement, the second objective of this project is to study the potential of multi-analyte detection in an integrated SPR device on glass. The first three chapters of the thesis are focused on the main objective. The design based on two different models is presented, at the same time as the related simulation tools. The first model is based on the weak coupling approximation and permits to obtain most of the information for the device’s design. The second model, having no approximation, is used to validate the first model and complete and refine the design. The fabrication process of the glass chip is then introduced, as well as the characterization instruments and protocols. A device is obtained, with a volumetric sensitivity between 1000 nm/RIU and 6000 nm/RIU depending on the analyte refractive index. The 3D integration of the waveguide within the glass substrate makes the device extremely compact and adapted to the integration with the microcalorimeter in particular. The last chapter describes the study of several spectral multiplexing techniques adapted to an integrated SPR system using the glass technology. The goal is to provide at least two simultaneous measurements. Several detection techniques are examined and the related devices are designed, fabricated and characterized.

Malgré le nombre croissant de capteurs dans les domaines de la chimie et la biologie, de nombreuses réactions n’ont pas encore été correctement identifiées et étudiées. C’est entre autres le cas des interactions intermoléculaires à l’interface liquide/solide trouvées dans les chimies de surface utilisées pour les méthodes de diagnostics médicaux et l’identification de divers processus biologiques. Afin de correctement comprendre les mécanismes en jeux, il est important de pouvoir croiser différentes méthodes de détection pour obtenir des informations complémentaires.MuLe principal objectif de cette étude est de dimensionner, fabriquer et caractériser un détecteur optique intégré sur verre basé sur la résonance plasmonique de surface, destiné à terme à être combiné avec d’autres techniques de détection. La résonance plasmonique de surface est une technique reconnue pour sa sensibilité adaptée à la détection de surface, qui a l’avantage d’être sans marquage et permet de fournir un suivi en temps réel de la cinétique d’une réaction. L’avantage principal de ce capteur est qu’il a été dimensionné pour une large gamme d’indice de réfraction de l’analyte, allant de 1,33 à 1,48. Ces valeurs correspondent à la plupart des entités biologiques associées à leurs couches d’accroche, particulièrement les matrices de polymères. Ces matrices sont de plus en plus utilisées non seulement pour leur capacité à augmenter la densité d’analytes présents à la surface du capteur, mais aussi pour leurs propriétés favorisant l’adsorption spécifique et leur utilisation comme élément actif de reconnaissance biologique.Étant donné que beaucoup d’études biologiques nécessitent la comparaison de la mesure à une référence ou à une autre mesure, le second objectif du projet est d’étudier le potentiel du système SPR intégré sur verre pour la détection multianalyte.MuLes trois premiers chapitres se concentrent sur l’objectif principal du projet. Le dimensionnement du dispositif suivant un cahier des charges préétabli est présenté, ainsi que les outils de simulation. Le procédé de fabrication de la puce optique sur verre est ensuite décrit, ainsi que les instruments et protocoles de caractérisation. Une comparaison est faite entre les simulations et les résultats expérimentaux, et les performances des outils numériques ainsi que celles du dispositif sont évaluées.Le dernier chapitre de la thèse présente l’étude de plusieurs techniques de multiplexage spectral adaptées à un système SPR intégré, exploitant en particulier la technologie sur verre. L’objectif est de fournir au moins deux détections simultanées. Dans ce cadre, plusieurs solutions sont proposées et les dispositifs associés sont dimensionnés, fabriqués et testés
In spite of the growing number of available biosensors, many biochemical reactions and biological components have not yet been studied in detail. Among them, some require the combination of several detection techniques in order to retrieve enough information to characterize them fully. An unknown reaction based, for example, on DNA hybridization could be characterized with an electrochemical sensor, a mechanical sensor and an optical sensor, each giving a different type of information.MuThe main objective of the work presented here is to design, fabricate and characterize a flexible integrated optical biosensor based on surface plasmon resonance, intended to be then combined with other detection techniques. Surface Plasmon Resonance (SPR) is well known to be a sensitive technique for surface-based biochemical detection. It has the advantage to be an unlabeled method and provides real time information on the kinetics of a reaction. The use of an integrated technology enables us to integrate several sensors on the same chip for the same sample, making them compact and low-cost. The flexibility of the proposed SPR biosensor comes from the fact that it is designed for a large range of analyte refractive indices, from 1.33 to 1.48 in the 600 nm-1000 nm wavelength range. These values are suitable for most biological entities and their ligand layers, and especially for hydrophilic polymer matrices used to trap DNA or protein entities. These biochemical matrices are used more and more for their ability to trap high densities of analyte, provide a strong binding and serve as an active detection medium with good anti-fouling properties.MuAs several biochemical studies require the simultaneous comparison of measurements to a reference or to another measurement, the second objective of this project is to study the potential of multianalyte detection in an integrated SPR device on glass.The first three chapters of the thesis are focused on the main objective. The design according to predefined specifications is presented, at the same time as the simulation tools. The fabrication process of the glass chip is introduced, as well as the characterization instruments and protocols. Simulation and experimental results are then compared, and the device performance is assessed.The last chapter describes the study of several spectral multiplexing techniques adapted to an integrated SPR system using the glass technology. The goal is to provide at least two simultaneous measurements. Several detection techniques are examined and the related devices are designed, fabricated and characterized

Cette thèse considère de nouvelles architectures prometteuses des métamatériaux plasmoniques pour biosensing, comprenant: (I) des réseaux périodiques 2D de nanoparticules d'Au, qui peuvent supporter des résonances des réseaux de surface couplées de manière diffractive; (II) Reseaux 3D à base de cristaux plasmoniques du type d'assemblage de bois. Une étude systématique des conditions d'excitation plasmonique, des propriétés et de la sensibilité à l'environnement local dans ces géométries métamatérielles est présentée. On montre que de tels réseaux peuvent combiner une très haute sensibilité spectrale (400 nm / RIU et 2600 nm / RIU, ensemble respectivement) et une sensibilité de phase exceptionnellement élevée (> 105 deg./RIU) et peuvent être utilisés pour améliorer l'état actuel de la technologie de biosensing the-art. Enfin, on propose une méthode de sondage du champ électrique excité par des nanostructures plasmoniques (nanoparticules uniques, dimères). On suppose que cette méthode aidera à concevoir des structures pour SERS (La spectroscopie du type Raman à surface renforcée), qui peut être utilisée comme une chaîne d'information supplémentaire à un biocapteur de transduction optique
This thesis consideres novel promissing architechtures of plasmonic metamaterial for biosensing, including: (I) 2D periodic arrays of Au nanoparticles, which can support diffractively coupled surface lattice resonances; (II) 3D periodic arrays based on woodpile-assembly plasmonic crystals, which can support novel delocalized plasmonic modes over 3D structure. A systematic study of conditions of plasmon excitation, properties and sensitivity to local environment is presented. It is shown that such arrays can combine very high spectral sensitivity (400nm/RIU and 2600 nm/RIU, respectively) and exceptionally high phase sensitivity (> 105 deg./RIU) and can be used for the improvement of current state-of-the-art biosensing technology. Finally, a method for probing electric field excited by plasmonic nanostructures (single nanoparticles, dimers) is proposed. It is implied that this method will help to design structures for SERS, which will later be used as an additional informational channel for biosensing