This thesis presents the development and application of nanoscale techniques to trap and / Chemistry and Chemical Biology

This thesis explores a novel methodology to fabricate three dimensional (3D) metal-dielectric structures, and two dimensional (2D) graphite layers for emerging metamaterials and graphene applications. The investigations we report here go beyond the limitations of conventional fabrication techniques that require multiple post-processing steps and/or are restricted to fabrication in two dimensions. Our method combines photoreduction mechanism with an ultrafast laser direct writing process in innovative ways. This study aims to open the doors to new ways of manufacturing nanoelectronic and nanophotonic devices. With an introductory analysis on how the various laser and chemical components affect the fabrication mechanism, this dissertation is divided into three sections. / Engineering and Applied Sciences

This thesis studies the different ways in which the localized plasmon heating effect of gold nanostructures -activated by plasmon excitation via visible and/or NIR irradiation- can be used to obtain different outcomes following the nanofabrication of applicable devices. Both spatial and temporal control were obtained for each one of the systems developed upon the incorporation of plasmonic gold nanostructures. Spatial control was enabled in hybrid mesoporous drug delivery systems fabricated in this thesis through the localized surface plasmon heating effect that allowed the modification of the dynamics of diffusion of the cargo being delivered, thus giving rise to different rates of release that can be controlled by plasmon excitation. At the same time, the plasmon heating effect proved to be capable of controlling the start of the release by dismantling thermo-responsive gates previously incorporated, thus enabling also a wavelength-controlled feature that enhances the versatility of these systems. Spatial control was also conferred to the photo-patterning applications presented in this dissertation by influencing the degree of motility of gold nanorods (AuNRs) embedded in polymer matrices allowing them to self-assemble when the longitudinal plasmon of the incorporated nanostructures was excited; the patterns generated were quite robust and persisted for extended periods of time. Finally, the feature of spatial heating control was also conferred to catalysis. The Friedel-Crafts alkylation of anisole by benzyl chloride using spherical gold nanoparticles (AuNPs) supported on Nb2O5-based catalysts was performed at bulk temperatures below those necessary for the reaction to occur when using bare or modified Nb2O5; this was the result of the combination of bulk and localized plasmon heating produced -both- via plasmon excitation. This also demonstrates the possibility of using plasmon excitation as an alternative heat source in this type of reactions. By combining the plasmonic properties of metallic nanostructures with those granted by mesoporous materials, polymer matrices and Nb2O5-based materials it was possible to obtain light-activated systems endowed also with temporal control and wavelength control while preserving the original properties of each systems' components. Overall, the content of this thesis describes in detail the practical aspects of combining gold nanostructures with different materials and the rationale behind the development of systems with customized and controllable properties.

La possibilité de fabriquer des dispositifs optiques pour la détection d’interactions chimiques,sans marquage et en temps réel, présente un intérêt croissant. Notamment, les cristaux photoniques(CPh) présentent un fort potentiel pour une telle application. Contrairement au silicium, majoritairementexploité pour la réalisation de telles structures, le diamant possède l’avantage d’avoir unesurface carbonée biocompatible permettant une fonctionnalisation covalente et stable de biomoléculesspécifiques. Dans ce contexte, cette thèse vise à étudier la potentialité qu’offre ce matériau pour la réalisationde CPh 2D destinés à des applications de biodétection. Pour cela, une plateforme photoniquemonolithique compacte, intégrable sur silicium et optimisée pour un fonctionnement aux longueursd’onde proches de 1.55 μm a été développée. Une géométrie de cavité à fente a été retenue afin demaximiser la sensibilité des structures photoniques à leur environnement extérieur. Des méthodesnumériques ont permis de préciser les paramètres géométriques des CPh. Des procédés de microstructurationde films minces de diamant polycristallin sur substrat silicium 2 pouces ont été développéset optimisés, pour aboutir à la réalisation de CPh caractérisés par des facteurs de qualité pouvantatteindre 6500. Deux procédés technologiques spécifiques aux films de diamant polycristallin ont notammentété développés : un procédé de lissage et un procédé de transfert de films de diamant surisolant. La sensibilité optique des CPh en diamant à une modification chimique de surface a ensuiteété étudiée et a tout d’abord montré une forte dépendance de leurs performances optiques à de simplesvariations des terminaisons chimiques du matériau. Par la suite, une preuve de concept de détectionsurfacique de protéines en milieu liquide par les CPh en diamant a été réalisée en utilisant le systèmede bioreconnaissance biotine/streptavidine, donnant une limite de détection estimée pour le systèmeà 10 μg/mL. Enfin, des travaux préliminaires de détection dans le visible ont été engagés via la réalisationde cavités à CPh fonctionnant à 600 nm, présentant déjà des facteurs de qualité dépassant les1500. / The ability to fabricate optical devices enabling the real time detection of chemical interactions,avoiding the use of markers, has motivated a growing interest. In particular, photonic crystals (PhC)based structures are promising candidates for such applications. Unlike silicon, that has currentlybeen used for most of these demonstrations, diamond offers a high stability and a versatile carbonsurface that can be functionalized to covalently bond specific organic or bio-molecules on its surface.In this context, this thesis aims at studying the interests of diamond for the realization of novel 2DPhC dedicated to biodetection applications. A fully monolithic compact photonic platform, integratedon silicon and optimized to work at wavelength of 1.55 μm was developed. A geometry consistingin a slotted cavity was chosen in order to maximize the sensitivity of such photonic structures totheir environment. Numerical methods allowed to determine the geometrical parameters of the PhC.Diamond microstructuration processes of polycrystalline diamond films deposited on two-inch siliconwafers were developed and optimized for the realization of PhC cavities with quality factors up to6500. Two technological processes specifically dedicated to polycrystalline diamond were developed : asmoothing process and a diamond layer on insulator integration by wafer bonding technology process.The optical sensitivity of diamond PhCs to simple surface modifications was studied and showed that,depending on the chemical surface termination, these diamond PhCs exhibit a strong modification oftheir spectral features. A proof of concept for surface detection in a water environment was realizedusing the biotin/streptavidin biorecognition system. The detection limit of the system was estimatedto be 10 μg/mL. Finally, first steps to detection in the visible range were made with the realization ofPhC working at 600 nm and exhibiting Q factors exceeding 1500.

In this thesis, the local field enhancement from multiple plasmonic structures were studied in different experiments. A new approach was applied to enhance the emission from upconverting nanoparticles to harvest energy from photons below the bandgap. A novel nanofabrication method was introduced to make double nanoholes for use in optical trapping, which was implemented to observe the nonlinear response from 2D materials and the enhanced emission from upconverting single nanoparticles. This method makes a large amount of apertures and is inexpensive. Selective plasmon-enhanced emission from erbium-doped nanoparticles using gold nanorods was demonstrated. Upconversion nanoparticles were excited with a dual-wavelength source of 1520~nm and 1210~nm simultaneously. The power dependence of the observed upconversion emission confirmed the contribution of both excitation bands in the upconversion process. Gold nanorods with resonances at 980~nm and 808~nm were implemented to selectively enhance the upconversion emission in order to harvest light with Si and GaAs solar cells, respectively. I also used colloidal lithography to fabricate double nanoholes which were plasmonic structures used for protein and nanoparticle trapping. This bottom-up technique enabled the fabrication of a large number of structures at low cost. Plasma etching of polystyrene nanoparticles using this technique tuned the cusp separation of double nanoholes down to 10~nm. The smaller cups separation enables to have more confined field in the gap which can be used in plasmonic sensing and plasmon enhanced upconversion processes. This technique can be used to fabricate plasmonic structures for nanoparticle trapping, spectroscopy, and sensing. In the next project, hexagonal boron nitride nanoflakes were trapped in a double nanohole fabricated with the colloidal lithography method. A second harmonic signal was detected at 486.5~nm where the particle was trapped and pumped with an ultra-low power laser at 973~nm. The power dependence measurements supported the second order process for second harmonic generation. Finite-difference time-domain (FDTD) simulations showed a 500-fold field intensity enhancement at the fundamental wavelength and a 450-fold enhancement in the Purcell factor at the second harmonic generation wavelength. This scheme is promising for ultra-fast imaging nonlinear optics technologies. In the last project, colloidal lithography double nanoholes were used to trap upconverting nanocrystals. Colloidal lithography double nanoholes with 32~nm cusp separation achieved 50 times larger emission compared to rectangular apertures. FDTD simulations showed the largest field enhancement in the aperture with the largest upconversion enhancement. 1550~nm emission from the trapped nanoparticle can be used as single-photon source. / Graduate

Nanomagnetic devices are highly energy efficient and non-volatile. Because of these two attributes, they are potential replacements to many currently used information processing technologies, and they have already been implemented in many different applications. This dissertation covers a study of nanomagnetic devices and their applications in various technologies for information processing – from simulating and analyzing the mechanisms behind the operation of the devices, to experimental investigations encompassing magnetic film growth for device components to nanomagnetic device fabrication and measurement of their performance. Theoretical sections of this dissertation include simulation-based modeling of perpendicular magnetic anisotropy magnetic tunnel junctions (p-MTJ) and low energy barrier nanomagnets (LBM) – both important devices for magnetic device-based information processing. First, we propose and analyze a precessionally switched p-MTJ based memory cell where data is written without any on-chip magnetic field that dissipates energy as low as 7.1 fJ. Next, probabilistic (p-) bits implemented with low energy barrier nanomagnets (LBMs) are also analyzed through simulations, and plots show that the probability curves are not affected much by reasonable variations in either thickness or lateral dimensions of the magnetic layers. Experimental sections of this dissertation comprise device fabrication aspects from the basics of material deposition to the application-based demonstration of an extreme sub-wavelength electromagnetic antenna. Magnetic tunnel junctions for memory cells and low barrier nanomagnets for probabilistic computing, in particular, require ultrathin ferromagnetic layers of uniform thickness, and non-uniform growth or variations in layer thickness can cause failures or other problems. Considerable attention was focused on developing methodologies for uniform thin film growth. Lastly, micro- and nano-fabrication methods are used to build an extreme sub-wavelength electromagnetic antenna implemented with an array of magnetostrictive nanomagnets elastically coupled to a piezoelectric substrate. The 50 pW signal measured from the approximately 250,000-nanomagnet antenna sample was 10 dB above the noise floor.

In this thesis by articles, I propose and demonstrate the full design, fabrication and characterization of optical biosensors based on (Bloch) Long Range Surface Plasmon Polaritons (LRSPPs). Gold waveguides embedded in CYTOP with an etched microfluidic channel supporting LRSPPs and gold waveguides on a one-dimensional photonic crystal (1DPC) supporting Bloch LRSPPs are exploited for biosensing applications. Straight gold waveguides embedded in CYTOP supporting LRSPPs as a biosensor, are initially used to measure the kinetics constants of protein-protein interactions. The kinetics constants are extracted from binding curves using the integrated rate equation. Linear and non-linear least squares analysis are employed to obtain the kinetics constants and the results are compared. The device is also used to demonstrate enhanced assay formats (sandwich and inhibition assays) and protein concentrations as low as 10 pg/ml in solution are detected with a signal-to-noise ratio of 20 using this new optical biosensor technology. CYTOP which has a refractive index close to water is the fluoropolymer of choice in current state of the art waveguide biosensors. CYTOP has a low glass transition temperature which introduces limitations in fabrication processes. A truncated 1D photonic crystal can replace a low-index polymer cladding such as CYTOP, to support Bloch LRSPPs within the bandgap of the 1DPC over a limited ranges of wavenumber and wavelength. Motivated by quality issues with end facets, we seek to use grating couplers in a broadside coupling scheme where a laser beam emerging from an optical fiber excites Bloch LRSPPs on a Au stripe on a truncated 1D photonic crystal. Adiabatic and non-adiabatic flared stripes accommodating wide gratings size-matched to an incident Gaussian beam are designed and compared to maximise the coupling efficiency to LRSPPs. The gratings are optimized, initially, through 2D modelling using the vectorial finite element method (FEM). Different 3D grating designs were then investigated via 3D modelling using the vectorial finite difference time domain (FDTD) method. Given their compatibility with planar technologies, gratings and waveguides can be integrated into arrays of biosensors enabling multi-channel biosensing. A multi-channel platform can provide, e.g., additional measurements to improve the reliability in a disease detection problem. Thus, a novel optical biosensor based on Bloch LRSPPs on waveguide arrays integrated with electrochemical biosensors is presented. The structures were fabricated on truncated 1D photonic crystals comprised of 15 period stack of alternating layers of SiO2/Ta2O5. The optical biosensors consist of Au stripes supporting Bloch LRSPPs and integrate grating couplers as input/output means. The Au stripes also operate as a working electrode in conjunction with a neighboring Pt counter electrode to form an electrochemical sensor. The structures were fabricated using bilayer lift-off photolithography and the gratings were fabricated using overlaid e-beam lithography. The planar waveguides are integrated into arrays capable of multichannel biosensing. The wafer is covered with CYTOP as the upper cladding with etched microfluidic channels, and wafer-bonded to a borofloat silica wafer to seal the fluidic channels and enable side fluidic interfaces. The proposed device is capable in principle of simultaneous optical and electrochemical sensing and could be used to address disease detection problems using a multimodal strategy.

Carbon nanotubes are appealing materials for nanofabrication due to their unique properties and structures. However, for carbon nanotubes to be used in mass-fabricated devices, precise control of nanotube orientation and location on surfaces is critical. I have developed a technique to align single-walled carbon nanotubes (SWNTs) on surfaces from a droplet of nanotube suspension under gas flow. Fluid motion studies indicate that alignment is likely due to circulation of SWNTs in the droplet. My work provides a facile method for generating oriented nanotubes for nanodevice applications. I have also devised an approach for localizing SWNTs onto 1-pyrenemethylamine-decorated DNA on surfaces. I found that 63% of SWNTs on surfaces were anchored along DNA, and these nanotubes covered ~5% of the total DNA length. This technique was an initial demonstration of DNA-templated SWNT localization. In an improved method to localize SWNTs on DNA templates, dodecyltrimethylammonium bromide was utilized to suspend SWNTs in aqueous media and localize them on DNA electrostatically. SWNT positioning was controlled by the surface DNA arrangement, and the extent of deposition was influenced by the SWNT concentration and number of treatments. Under optimized conditions, 83% of the length of surface DNAs was covered with SWNTs, and 76% of the deposited SWNTs were on DNA. In some regions, nearly continuous SWNT assemblies were formed. This approach should be useful for the fabrication of nanotube nanowires in nanoelectronic circuits. Using my improved procedures, I have localized SWNTs on DNA templates across electrodes and measured the electrical properties of DNA-templated SWNT assemblies. When a DNA-templated SWNT was deposited on top of and bridging electrodes, the measured conductance was comparable to literature values. In contrast, SWNTs with end-on contacts to the sides of electrodes had conductances hundreds of times lower than literature values, probably due to gaps between the SWNT ends and the electrodes. This work provides a novel approach for localizing SWNTs across contacts in a controlled manner. These results may be useful in the fabrication of nanoelectronic devices such as transistors with SWNTs as active components. Moreover, this approach could be valuable in arranging SWNTs as electrical interconnects for nanoelectronics applications.

Bottom-up self-assembly can be used to create structures with sub-20 nm feature sizes or materials with advanced electrical properties. Here I demonstrate processes to enable such self-assembling systems including block copolymers and DNA origami, to be integrated into nanoelectronic devices. Additionally, I present a method which utilizes the high stability and electrical conductivity of graphene, which is a material formed using a bottom-up growth process, to create archival data storage devices. Specifically, I show a technique using block copolymer micelle lithography to fabricate arrays of 5 nm gold nanoparticles, which are chemically modified with a single-stranded DNA molecule and used to chemically attach DNA origami to a surface. Next, I demonstrate a method using electron beam lithography to control location of nanoparticles templated by block copolymer micelles, which can be used to enable precise position of DNA origami on a surface. To allow fabrication of conductive structures from a DNA origami template, I show a method using site-specific attachment of gold nanoparticles to and a subsequent metallization step to form continuous nanowires. Next, I demonstrate a long-term data storage method using nanoscale graphene fuses. Top-down electron beam lithography was used to pattern atomically thin sheets of graphene into nanofuses. To program the fuses, graphene is oxidized as the temperature of the fuse is raised via joule heating under a sufficiently high applied voltage. Finally, I investigate the effect of the fuse geometry and the electrical and thermal properties of the fuse material on the programming requirements of nanoscale fuses. Programming voltages and expected fuse temperatures obtained from finite element analysis simulations and a simple analytical model were compared with fuses fabricated from tellurium, a tellurium alloy, and tungsten.

<p>Transition metal dichalcogenides (TMDs) have attracted significant attention in recent years with their immense potential to revolutionize optoelectronics and electrochemical energy applications. However, several challenges have prevented their practical use, including fabrication difficulties, incompatibility with conventional doping techniques, and unwanted environmental effects. This thesis aims to address the issues by introducing novel strategies for transforming TMDs into organic-integrated hybrid structures. Furthermore, this study focuses on gaining a fundamental understanding and a tunability of the unique physical properties of TMDs. Finally, to unlock their full potential, this thesis explores synergetic effects among the hybrid components for the development of advanced optoelectronics and energy devices. </p> <p><br></p> <p>By combining atomically thin TMDs with uniform organic layers, we have developed various two-dimensional (2D) hybrid junctions, including TMD/organic, TMD/TMD/organic, and TMD/organic/TMD. The TMD/organic hybrids are designed for type-II energy band alignments at the heterointerface and exhibit significantly improved (photo)conductivity and uniform photoresponse compared to pristine TMDs. The optoelectronic characteristics vary as a function of the layer number of TMDs, one of the unique features of ultrathin materials. We also find that integrating organic layers can tailor the charge density and polarity of TMD flakes, thus enabling controllable doping without damaging the crystallinity. </p> <p><br></p> <p>The hybrid approach not only modulates the properties of individual TMD layers but also offers an opportunity to study unique phenomena of 2D heterostructures such as interlayer excitons (XIs). XIs are spatially separated bound states of an electron and a hole in TMD/TMD heterolayers. We prepared various TMD/TMD/organic hybrid heterostructures with distinct energy band alignments and demonstrated a selective modulation of XI emission. The photoluminescence from the radiative recombination of XIs can be preserved, quenched, or modulated based on the band alignments. Furthermore, we fabricated organic-layer-inserted heterolayers (TMD/organic/TMD) and investigated the environmental effects on XIs. The organic layers tailor the dielectric screening within XIs and the dipolar interaction among XIs, thus regulating the energy states of XIs.</p> <p> </p> <p>In addition to the rich potential in optoelectronics, the hybrid strategies are advantageous to improve electrochemical energy storage. We constructed hybrid composites from core carbon nanotubes, intermediate metal-organic frameworks (MOFs), and outer TMD layers for supercapacitor electrodes. The 3D hierarchical composites aim to achieve synergetic effects from the components and offer high energy density while maintaining excellent power density and durability. Percolated nanotube networks are highly conductive, MOFs ensure a fast ion diffusivity, and TMD offers a large ion capacity. We engineered the TMD morphologies via topochemical synthesis and determined the optimal structure maximizing faradaic-reactive surface areas for improved ion accumulation and redox energy storage. We found that the hybrid composite of a flower-like TMD structure interwoven with carbon networks exhibits an unprecedentedly high energy density of over 80 Wh/kg, superior to conventional supercapacitors. </p> <p><br></p> <p>In summary, this thesis presents powerful strategies for engineering atomically thin TMDs and critical insights on relevant physics which may not be accessible otherwise. Given the extensive library of organic molecules, the hybrid approach may provide a versatile platform to study 2D materials and open new opportunities. The findings could serve as the foundation for the development of novel optoelectronic and energy storage applications.</p>