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In this study, sharp/gradual converging-diverging microchannels with contraction/ expansion ratio of 4:1/1:4 was designed to generate elongational flow with uniform velocity in the centerline. The £f-DNA stained with YOYO-1 was observed in the flow. MPIV was built to measure the velocity distribution and local strain rate was estimated by MPIV measurements. The deformation and conformation of individual DNA molecules in the flow was visualized with confocal laser scanning microscopy (CLSM). The goal of the present work was to develop a method for stretching DNA molecules, in order to perform analysis of coil-stretch transition of DNA. By measuring dynamic properties and relaxation time of DNA molecules stretched by pressure driven at various flow rate and viscosity, we have shown how one could investigate the influence of hydrodynamic interactions in the case of stretching of DNA molecules.

In this study, we design different inscribed/circumscribed circular torus-type microchannels to investigate the stretching behavior of DNA molecules. Strain rate and relaxation time play an important role in DNA stretching. In order to perform an analysis of the coil-stretch transition of DNA, we develop a method of stretching DNA molecules by using £gPIV and CLSM measurements. £gPIV is designed to measure the velocity distribution, after which the local strain rate can be estimated. The hydrodynamic stretching of DNA molecules in the elongation flow is observed using a confocal laser scanning microscope (CLSM). The relaxation time of the DNA molecules is then estimated according to the CLSM images analysis. At present, our experiments using the electro-osmotic flow (EOF) driven at various electric fields and viscosities to stretch DNA molecules show how one can investigate the influence of hydrodynamic interactions in the case of stretching of DNA molecules.

Carbon nanotubes have unique electronic, optical, mechanical, and transport properties which make them an important element of nanoscience and nanotechnology. However, successful application and integration of carbon nanotubes into new nanodevices requires fundamental understanding of their property changes under the influence of many external factors. This dissertation presents qualitative and quantitative theoretical understanding of property changes, while carbon nanotubes are exposed to the deformations, defects, external electric fields, and adsorption. Adsorption mechanisms due to Van der Waals dispersion forces are analyzed first for the interactions of graphitic materials and biological molecules with carbon nanotubes. In particular, the calculations are performed for the carbon nanotubes and graphene nanoribbons, DNA bases, and their radicals on the surface of carbon nanotubes in terms of binding energies, structural changes, and electronic properties alterations. The results have shown the importance of many-body effects and discrete nature of system, which are commonly neglected in many calculations for Van der Waals forces in the nanotube interactions with other materials at nanoscale. Then, the effect of the simultaneous application of two external factors, such as radial deformation and different defects (a Stone Wales, nitrogen impurity, and mono-vacancy) on properties of carbon nanotubes is studied. The results reveal significant changes in mechanical, electrical, and magnetic characteristics of nanotubes. The complicated interplay between radial deformation and different kinds of defects leads to the appearance of magnetism in carbon nanotubes which does not exist in perfect ones. Moreover, the combined effect of radial deformation and external electric fields on their electronic properties is shown for the first time. As a result, metal-semiconductor or semiconductor-metal transitions occur and are strongly correlated with the strength and direction of external electric field and the degree of radial deformations.

One of the main subjects of this thesis is to design a novel synthetic route to covalently functionalize carbon nanotubes with various molecules in a non-toxic way on both surface and suspension. Functionalized carbon nanotubes are of great interest in the field of molecular electronics, materials science and nano-bio applications because of their remarkable structural, chemical and physical properties. First, the single-walled carbon nanotubes are functionalized with gold nanoparticles by the route, which involves silanization and copper-free click chemistry (SPAAC). We characterize the functionalized nanotubes through XPS, IR and Raman spectroscopic techniques to identify the surface attachment of molecules after each step. We observe a drastic change in homogeneity and functionalization density of single-walled carbon nanotubes with gold nanoparticles concerning solvent through TEM. Employing the same route, biomolecules such as fluorescent dyes and single-stranded DNA molecules are integrated with SWNTs. Fluorescence lifetime analysis of AF647 functionalized SWNTs is reduced compared to free dye due to the fluorescence quenching phenomenon of carbon nanotubes. Functionalized SWNTs are characterized with FLIM, SEM, and Raman for better correlation at the same area of interest. Furthermore, the nanotubes are resolved at the nanoscale level through STORM imaging technique with a limited photon budget. Single-stranded DNA molecules of different lengths are used to investigate the fluorescence quenching as they are distance-dependent. DNA-PAINT is engaged in imaging the functionalized SWNTs with an unlimited photon budget, overcoming STORM's challenge. Lastly, the route is transferred to surface-grown CNTs through the CVD technique, in which both the gold nanoparticles and fluorescent dyes are grafted with nanotubes selectively. CVD is carried out on different substrates Si/SiO2, quartz substrate and quartz coverslip for substrate functionalization. Catalyst deposition plays a significant role in not only the CVD growth but also in the lifetime analysis of the substrate functionalized nanotubes. We observe similar fluorescence quenching of nanotubes in the substrate compared with nanotubes functionalized in suspension. Surface-grown nanotubes in the optically transparent substrate can be resolved through STORM at the nanoscale level. In conclusion, we demonstrate a synthetic design to functionalize SWNTs which provides the possibility to be versatile and non-toxic. Moreover, we show that the nanotubes can be functionalized through this route homogeneously and selectively on both surface and suspension. This work lays the foundation for tailoring SWNTs with not only a wide range of molecules and to study their functional characteristics but also to carry out functionalization on different substrates for various applications.

Un échange vigoureux au travers des frontières de la biologie et de la physique se développe autour de nouvelles méthodes et outils, et autour de nouveaux phénomènes. Les objets d’étude au cœur de ce recouvrement multidisciplinaire sont très divers. De manière non exhaustive, il s’agit de nanoparticules, de cellules ou encore d’objets encore plus petits et élémentaires tels que les molécules. Aussi bien pour des applications dans le domaine de la microélectronique que pour l’étude de mécanismes biologiques fondamentaux, l’intégration des objets d’intérêt à l’échelle de l’objet unique est essentielle. Dans le cadre de cette thèse, l’objectif que nous nous sommes fixés est de développer un volet technologique qui permette l’assemblage d’objets micro- ou nanométriques uniques à des endroits bien définis d’une surface solide de façon simple, fiable, bas-coût et parallèle. Pour ce développement, nous nous sommes intéressés tout particulièrement aux nanoparticules d’Au de 100 nm de diamètre, aux bactéries, puis aux molécules d’ADN. Nous décrirons les stratégies développées reposant sur la lithographie douce puis leurs potentialités pour différentes applications dans les domaines de l’analyse médicale et de la détection. / A vigorous trade across the borders of biological and physical sciences is developing around new methods and tools, and around new phenomena. The objects at the heart of this multidisciplinary overlapping are numerous. In a non exhaustive manner, the objects of study can be nanoparticles, cells, or even smaller and more elementary objects such as molecules. For applications in the field of microelectronics as for studies of fundamental biological mechanisms, the integration of these objects of interest at the single object scale is essential. In the frame of this Ph.D. thesis, the objective we pursued is the development of a technological tool-box allowing the assembly of micro- and nano-objects at pre-determined locations of a solid surface, in a simple, reliable, low-cost and parallel manner. For this development, we focused on gold nanoparticles 100 nm in diameter, bacterial cells and DNA molecules in particular. We will describe the strategies developed relying on soft-lithography and their potentialities for different applications in the fields of medical analysis and sensing.

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