Depuis l'apparition du terme "biosensor" à travers un article de Lyons et Clark en 1962, les biocapteurs ont connu un véritable essor tant au niveau académique qu'industriel. Le principal objectif de ce travail de thèse était de créer une surface permettant l'immobilisation spécifique par liaison covalente de simple ou double brin d'ADN puis d'étudier les interactions pouvant exister entre une protéine donnée et l'ADN. Pour préparer la surface à cette immobilisation, nous avons opéré une réduction électrochimique de sel d'aryldiazoniums. Ce type de modification nous a permis de fixer de manière covalente sur la surface conductrice des fonctions de type Ar-SO2Cl. Par l'utilisation de la QCM et de l'AFM, nous avons pu par la suite détailler les mécanismes de fonctionnement de protéines (HsRad51 et Transposase) en interaction avec l'ADN simple ou double brin fixé, que ce soit d'un point de vue cinétique ou bien structural. / Since the emergence of the term "biosensor" through an article of Clark and Lyons in 1962, such devices have experienced a tremendous activity both in the academic and industries. The main objective of this thesis work was to create a surface allowing the specific immobilization of single or double DNA strand by covalent bonding and then study the interactions that may exist between a given protein and DNA. To functionalize the surface, we firstly investigated the electrochemical reduction of aryldiazoniums salt. This kind of methodology has allowed us to covalently graft Ar-SO2Cl functions over the conductive surface which can further react with DNA to immobilize it. By using the QCM and AFM methodologies, we are able to kinetically or structurally detail the intimate mechanisms of interactions between two proteins (HsRad51 and Transposase) and single or double strand DNAs.

Un microscope à force atomique (AFM) est utilisé pour caractériser des matériaux isolant ou semi-conducteur avec une résolution pouvant atteindre l'échelle atomique. Ce microscope est constitué d'un capteur de force couplé à une électronique de contrôle pour pouvoir correctement caractériser ces matériaux. Parmi les différents modes (statique et dynamique), nous nous focalisons essentiellement sur le mode dynamique et plus particulièrement sur le fonctionnement sans contact à modulation de fréquence (FM-AFM). Dans ce mode, le capteur de force est maintenu comme un oscillateur harmonique par le système d'asservissement. Le projet ANR Pnano2008 intitulé : ”Cantilevers en carbure de silicium à piézorésistivité métallique pour AFM dynamique à très haute fréquence" a pour objectif d'augmenter significativement les performances d'un FM-AFM en développant un nouveau capteur de force très haute fréquence. Le but est d'augmenter la sensibilité du capteur et de diminuer le temps nécessaire à l'obtention d'une image de la surface du matériau. Le système de contrôle associé doit être capable de détecter des variations de fréquence de 100mHz pour une fréquence de résonance de 50MHz. Etant donné que les systèmes présents dans l'état de l'art ne permettent pas d'atteindre ces performances, l'objectif de cette thèse fut de développer un nouveau système de contrôle. Celui-ci est entièrement numérique et il est implémenté sur une carte de prototypage basée sur un FPGA. Dans ce mémoire, nous présentons le fonctionnement global du système ainsi que ses caractéristiques principales. Elles portent sur la détection de l'écart de fréquence de résonance du capteur de force. / An atomic force microscope (AFM) is used to characterize insulating materials or semiconductors with a resolution up to the atomic length scale. The microscope includes a force sensor linked to a control electronic in order to properly characterize these materials. Among the various modes (static and dynamic), we focus mainly on the dynamic mode and especially on the frequency modulation mode (FM-AFM). In this mode, the force sensor is maintained as a harmonic oscillator by the servo system. The research project ANR Pnano2008 entitled: "metal piezoresistivity silicon carbide cantilever for very high frequency dynamic AFM" aims to significantly increase the performance of a FM-AFM by developing new very high frequency force sensors. The goal is to increase the sensitivity of the sensor and to decrease the time necessary to obtain topography images of the material. The control system of this new sensor must be able to detect frequency variations as small as 100mHz for cantilevers with resonance frequencies up to 50MHz. Since the state-of-the-art systems doe not present these performances, the objective of this thesis was to develop a new control system. It is fully digital and it is implemented on a FPGA based prototyping board. In this report, we present the system overall functioning and its main features which are related to the cantilever resonant frequency detection. This detection is managed by a phase locked loop (PLL) which is the key element of the system.

ABSTRACT The focus of this work was the study possible ways to improve the efficiency of solar cells. To this end, the main aim was to investigate the deposition process of Indium Tin Oxide (ITO), Titanium Dioxide (TiO2), multi-layers ITO/TiO2 on quartz SiO2 substrates under different conditions (oxygen pressure, laser fluence and wavelength, and temperature) and later gold nanoparticles by the Reactive Pulsed Laser Ablation Deposition (RPLAD) technique. It was intended to investigate their electrical structural and optical properties under selected conditions for possible application to Dye Sensitised Solar Cells (DSSC). Under optimised conditions, maximum deposition rates of 12nm/min for ITO and 21nm/min for TiO2 thin films were achieved. Rutherford Backscattering Spectrometry (RBS) with 2MeV He+ ions was used to measure the films thickness. Uniform thicknesses over a large area were found to be about 400nm and 800nm for ITO and TiO2 films, respectively. Crystalline properties were studied via x-ray diffraction and Raman spectroscopy. X-ray Diffraction (XRD) analysis revealed that the ITO films are highly orientated nanocrystals with their a-axis normal to the glass substrate surface. The average particle size of the precipitated nanocrystals was calculated to be 10-15nm. The structure of the films was characterised via Atomic Force Microscopy (AFM) imaging of the top surface of the film. The films have a rough surface with average roughness of 26-30nm. Pores were observed with a density of 144 and 125 pores/mm2 and average size of 150 and 110nm for ITO films deposited at 200 and 400°C, respectively. TiO2 films deposited on the prepared ITO films were less crystalline. Annealing was performed at 300 and 500°C for 3 consecutive hours and the XRD results show that the transformation of TiO2 film into anatase phase was almost complete with a crystal size of ~ 6-7nm. Scanning Transmission Electron Microscopy (STEM) of the surfaces was also performed. The TiO2 films deposited onto the prepared ITO films present a relatively high pore size with an average pore diameter of ~ 40nm and excellent uniformity. It is interesting to note that the pores are randomly arranged. The random arrangement of the pores network may actually be beneficial for producing a uniform electrode. In addition, STEM cross-sectional analysis of the films showed a columnar structure but no evidence of voids in the structure. The large surface area produced suggests applications in DSSC. The electrical properties of the films were investigated and an estimation of resistivity and Hall mobility was made. Low values of resistivity and high values of mobility were observed for ITO films. The resistivity of the film increases with increasing thickness while it decreases when increasing the deposition temperature. The lowest value was found to be 1.5x10-6Ωm for ITO films deposited at 400°C. Hall mobility was found to increase with substrate temperature. In this investigation, the highest Hall mobility at room temperature was estimated to be 22.3cm2/Vs under ambient O2 pressure (PO2) of 1Pa and 52.1 and 51.3cm2/Vs for films deposited at 200 and 400°C, respectively. But the best ITO film was deposited at 200°C, since this film combines good resistivity, good Hall mobility and good transmittance. UV-VIS-IR transmission spectra were recorded on a Perkin Elmer Lambda 900. From the transmission data, the energy gap as well as the optical constant was estimated. A high transmission for ITO films in the visible (Vis) range was observed which was above 88% for films produced at room temperature and above 95% for those deposited at 200°C. The transmission for the films produced in oxygen was about 90% above 400nm, whereas it lies between 70 and 80% for films produced in rare gases. An increase in the band gap was observed by increasing the oxygen pressure and substrate temperature for ITO films. Increasing the quartz SiO2 substrate temperature from room temperature to 400 °C resulted in an increase of the transmission of TiO2 films, mostly in the Visible Near Infrared (Vis-NIR) from about 70% to 92%. After annealing at 500°C for 3 consecutive hours, the transmission of TiO2 film further sharply decreases toward shorter wavelengths. Analysis of the transmittance curve of TiO2/Au shows a decrease of about 6% of the transmission in the Ultraviolet Visible (UV-Vis) range. Optical absorption edge analysis showed that the optical density could be used to detect the film growth conditions and to correlate the film structure and the absorption edge. The TiO2 films deposited present a direct band gap at 3.51eV and 3.37eV for TiO2 as deposited and after annealing, respectively, while the indirect band gap was found to be 3.55eV and 3.26eV for TiO2 films as deposited and after annealing, respectively. There was a shift of about 0.1eV between as deposited ITO monolayer films and ITO/TiO2 bilayers deposited at 200°C. A small shift towards shorter wavelengths has been observed for multilayer ITO/TiO2/Au. In this case, the increase of Eg was ascribed to a reduction of the oxygen vacancies with increasing substrate temperature at which the ITO film was deposited. The change in the shape of the fundamental absorption edge is considered to reflect the variation of density and the short range structural modifications undetected by structural characterisations. Enlargement of band-gap energies of semiconductors may be advantageous when used in DSSC to suppress the charge recombination between the reduced electrolytes and the photo-excited holes in the valence band of TiO2 substrates and enhance the open-circuit potential of the cell. When ITO/TiO2 bilayers were annealed before depositing Au, the gap energy remained constant.

Neste trabalho foram estudadas as propriedades de adsorção de poli(omethoxianilina) (POMA) em filmes automontados, nos quais camadas de POMA foram alternadas com camadas de ácido polivinil sulfônico (PVS). Devido à baixa solubilidade da POMA, o método de preparação das soluções aquosas de POMA interfere nas características da adsorção. Para POMA com controle de massa molar, que contém fração de alta massa, a cinética de adsorção de uma camada de POMA em filmes de POMAlPVS obedece a um processo de dois estágios. O primeiro é um processo de primeira ordem enquanto o segundo é descrito pela função de Johnson-Mehl-Avrami com n=1, característico de crescimento de bastões. Este tipo de crescimento foi confirmado através de análises do tamanho dos agregados em medidas de microscopia de força atômica (AFM). As propriedades morfológicas desses filmes POMAlPVS foram analisadas usando leis de escala, onde a dimensão fractal foi 2.2, indicando adsorção self-affine. Para POMA polidispersa sem controle da massa molar, a quantidade de material adsorvido aumenta não monotonicamente com o tempo devido à competição entre os mecanismos de adsorção e dessorção. Tal competição foi também manifestada nas propriedades morfológicas, com o tamanho do grão nos filmes de POMAlPVS aumentando não monotonicamente com o tempo. A importância das ligações de hidrogênio no mecanismo de adsorção para POMA foi demonstrada em alguns experimentos. Por exemplo, foi mostrado que a adsorção é eficiente para soluções de POMA com pH 5 em que a POMA não está dopada e, portanto a atração iônica não pode ser responsável pela adsorção. Além disso, observou-se adsorção não autolimitada da POMA, a qual depende das interrupções no processo de adsorção. Foi notada, através de medidas de calorimetria de varredura diferencial (DSC), a presença de água no pó de POMA e em filmes automontados POMAlPVS sobre esferas de sílica. A energia de adsorção variou de 6 a 15 kcallmol, que pode ser atribuída a ligações de hidrogênio. Devido a ligações de H a quantidade de material adsorvido aumenta com o número de bicamadas, e isto é refletido na isoterma de adsorção da POMA. As isotermas foram analisadas com o modelo de Filippova que descreve a cinética de adsorção de polieletrólitos em uma superfícies plana, e permite obter energias de ativação para as interações entre polieletrólitos/polieletrólitos, polieletrólitoslinterface e polieletrólitos/solvente. A energia de interação entre as moléculas adsorvidas no substrato (vidro ou filme automontado com bicamadas de POMAlPVS) aumenta com o número de bicamadas de 0.9 kcallmol para substrato de vidro a 5.39 kcal/mol para uma camada de POMA adsorvida em um filme com 10 bicamadas de POMAlPVS / This thesis addresses the adsorption properties of poly(o-methoxyaniline) (POMA) in layer-by-Iayer (LBL) films, for which POMA layers were alternated with layers of the polyanionic poly(vinylsulfonicacid) (PVS). Due to the reduced solubility of POMA, the method of preparation of POMA aqueous solution sinterfered in the adsorption characteristics. For POMA with controlled mass, which contained high molecular weight fractions, the kinetics of adsorption of a POMA layer on already deposited POMA/PVS films obeyed a two-step process. The first process is a firs torder kinetics process while the second one is described by the Johnson-Mehl-Avrami function with n = 1, characteristic of preferential growth of cylinders. This growth was confirmed in the analysis of aggregate size in atomic force microscopy (AFM) measurements. The morphological properties of these POMA/PVS films were analyzed using scaling laws, where the fractal dimension was approximately 2.2, denoting self-affine adsorption. For polydisperse POMA with no control of \"molecular weight\", the amount of material adsorbed increased non-monotonically with time due to a competition between adsorption and desorption mechanisms. Such competition was also manifested in themorphological properties, with the grain size in POMA/PVS films increasing non-monotonically with time. The importance of H-bonding in the adsorption mechanisms for POMA was demonstrated in several instances. For example, it is shown that POMA adsorption is efficient for solutions with pH 5 where POMA is not doped and therefore ionic attraction cannot be held responsible for adsorption. Moreover, non-self-limited adsorption of POMA was demonstrated, which depended on the interruptions in the adsorption process. H-bonding probably occurs in entrained water, which was shown to be present in POMA powder and in POMA/PVS films deposited on silica particles, using differential scanning calorimetry (DSC). Activation energies of 6-15 kcal/mol were estimated, which can be attributed to H-bonding. Because of H-bonding interactions the amount of material adsorbed increases with the number of bilayers, and this is reflected in the adsorption isotherms for POMA. The latter were analyzed with Fillippova\'s model in which the adsorption kinetics of polyelectrolytes on a planar surface is described. It allows estimation of activation energies characterizing interactions between polyelectrolyte/polyelectrolyte, polyelectrolyte/interface and polyelectrolyte/solvent. The energy of interaction between the molecules to be adsorbed and the substrate (bare or coated with POMA/PVS layers) increases with the number of bilayers, from 0.9 kcal/mol for the bare substrate to 5.39 kcal/mol for a POMA layer adsorbed on a 10-bilayer POMA/PVS film

INTRODUÇÃO: A qualidade da interface osso-implante pode ser influenciada diretamente pela rugosidade da superfície e determina a forma como as células interagem, aderem-se e fixam-se a ela, podendo potencializar e encurtar o tempo de osseointegração. Este estudo propôs-se analisar qualitativamente a topografia e arquitetura de diferentes superfícies de implantes dentários, compará-las, descrevê-las e correlacioná-las com os possíveis eventos moleculares e celulares iniciais da osseointegração. MATERIAIS E MÉTODOS: cinco implantes com diferentes tratamentos de superfície foram analisados em três diferentes áreas: apical, região de roscas (topos, flancos e vales) e região cervical por microscopia eletrônica de varredura (MEV) e topo do ápice em microscopia de força atômica (MFA). RESULTADOS: as superfícies dos implantes NanoTite®, SLA® e Xive® TG plus, no MEV, são semelhantes pelo seu aspecto de lacunas, diferindo no plano superficial; a superfície do implantes TiUnite® apresenta características coraliformes/vulcanoides, enquanto a do implante Exopro® apresenta estrias em formas de pequenos sulcos. A rugosidade média (Ra) à MFA, apresentou-se maior no implante TiUnite®, seguido pelos implantes Xive®TG plus, NanoTite®, Exopro® e SLA®. A área analisada se restringe a pequenos pontos (nanométricos), que não possibilita uma visão panorâmica de todas as estruturas (micrométricas), e consequentemente não permite uma real comparação da rugosidade. CONCLUSÕES: a metodologia ideal para análise das superfícies com o objetivo de compreender como as células às colonizam e se aderem deve ser em escala micrométrica, destacando-se à MEV em detrimento da MFA. As duas metodologias, MEV e MFA, são fundamentais na análise de superfície de implantes dentários, porém devem ser conjuntamente e/ou simultaneamente empregadas. A MFA parece ser a mais adequada para estudos que visem a interação da superfície dos implantes com estrutura de nível molecular e à MEV, no nível celular. Cada tratamento de superfície promove um tipo específico de topografia, cujos benefícios moleculares, teciduais e clínicos devem ser estudados caso a caso. / Introduction: Bone-implant interface quality may be influenced by surface roughness and determines how cells interact, cling to and fix to, therefore can enhance and shorten the time for osseointegration. This study aims to analyze qualitatively the topography and architecture of different dental implants surfaces, to compare and describe them. MATERIALS AND METHODS: five implants with different surface treatments were evaluated in three different areas: apical, region of threads (tops, sides and valleys) and cervical region by scanning electron microscopy (SEM) and atomic force microscopy (AFM), correlating the possible molecular and cellular initials events of osseointegration. RESULTS: the surfaces of the implants NanoTite®, SLA® and ® Xive® TG plus, in the SEM, are similar by their appearance of gaps, although they differ in surface plane; the surface of TiUnite® implants have features such as corals and/or volcanos, while the implant Exopro ® has stretch marks in form of small grooves. The average roughness (Ra) to the AFM, appeared higher in TiUnite ® implant, followed by Xive® TG plus NanoTite®, Exopro® and SLA® implants. The area analyzed in the AFM, is restricted to small points (nanometrics), and do not allow denote a panoramic view of all structures (micrometrics), not allowing a real comparison of surface roughness. CONCLUSIONS: the optimal methodology for surfaces analysis with the objective of understanding how the cells colonize and fix to dental implants should be in the micrometer scale, highlighting the SEM over AFM. The AFM seems to be most suitable for studies aiming the interaction of the implant surface with molecular-level and SEM at the cellular level. Each treatment promotes a specific surface topography whose benefits molecular, tissue, and clinical should be studied separately.

A crescente preocupação com o desenvolvimento sustentável, aliada com uma maior conscientização com relação à preservação do meio ambiente, tem incentivado pesquisas com a finalidade de encontrar substitutos ambientalmente amigáveis para os eficientes sistemas à base de cromo hexavalente (Cr6+), que são empregados como pré-tratamento em ligas de alumínio de alta resistência utilizadas na indústria aeronáutica. Neste trabalho, o desempenho do silano BTSE (Bis-1,2-(trietoxisilil) etano) como método de proteção contra a corrosão da liga de alumínio 2024-T3 foi investigado utilizando técnicas de caracterização eletroquímicas, microestruturais e químicas. Para melhorar as propriedades anticorrosivas do sistema, a camada de silano foi modificada pela introdução de aditivos, tendo sido estudados também sistemas em bi-camada. Efeitos das condições de cura (tempo e temperatura) do BTSE e da quantidade de modificantes sobre as propriedades dos substratos revestidos também foram avaliados. Para os estudos eletroquímicos, realizados em solução de NaCl 0,1 M, foram empregadas a espectroscopia de impedância eletroquímica (EIS) e curvas de polarização potenciodinâmica anódica e catódica. As técnicas de caracterização morfológica e microestrutural foram microscopia de força atômica (AFM), microscopia eletrônica de varredura (SEM) e medidas de ângulo de contato. A caracterização da composição e do estado químico da camada foi realizada usando as espectroscopias por energia dispersiva de Raios-X (EDS), de infravermelho (IR) e de fotoelétrons excitados (XPS). Os resultados dos ensaios de corrosão mostraram que a adição dos modificantes à camada de BTSE melhora o desempenho anticorrosivo do sistema, o qual também teve seu comportamento melhorado quando utilizado em forma de bi-camada. Verificou-se que um excesso de aditivos tende a deteriorar as propriedades protetoras do silano, e que o aumento do tempo e da temperatura de cura é benéfico para as propriedades anticorrosivas dos diferentes sistemas. Os resultados dos ensaios de caracterização química e microestrutural também detectaram que os modificantes contribuem para uma melhor cobertura do substrato pela camada de silano, assim como para uma maior reticulação da mesma, sem, no entanto, modificar sua estrutura química e física. / The increasing concern with sustainable development, allied with a stronger awareness with environmental preservation, has stimulated researches in order to find environmentally friendly substitutes to replace the efficient hexavalent chromium-based pre-treatment systems (Cr6+) used to protect high-strength aluminium alloys employed in the aircraft industry. In this work, the performance of BTSE (bis-1, 2-(triethoxysilyl) ethane) as a protection method against corrosion of aluminium alloy 2024-T3 was investigated using electrochemical, microstructural and chemical characterization techniques. In order to improve the system anticorrosion properties, modifiers were added to the silane layer, and bi-layers systems were also tested. The effects of the silane curing conditions (time and temperature) and of the modifiers amounts on the properties of the layers were also evaluated. Electrochemical impedance spectroscopy (EIS) and anodic and cathodic potentiodynamic polarization curves were employed for the electrochemical studies, which were performed in 0.1 M NaCl solution. For microstructural and morphological characterization, atomic force microscopy (AFM), scanning electron microscopy (SEM) and contact angle measurements were used. The chemical state and the composition of the different layers were evaluated using X-ray photoelectrons (XPS), infrared (IR) and X-ray dispersive energy (EDS) spectroscopy. The results of the corrosion studies have shown that the addition of modifiers to the BTSE layer improves its anticorrosion performance, which was also improved in the bi-layers systems. It was also verified that addition of modifiers excess hinders the performance of the layers, as well as that increasing curing time and temperature are beneficial to the anticorrosion properties of the systems. The results of the different chemical and microstructural analyses showed that the modifiers contribute to better substrate coverage by the silane layer, as well as to a more complete reticulation. However, this does not imply in modifications of the chemical and physical structure of the layer.

"Polyelectrolyte multilayer (PEM) thin films prepared via the Layer-by-Layer (LbL) deposition technique are of special interest in this research. The purpose of this study is to replace current mechanical closure systems, based on hook-and-loop type fasteners (i.e. Velcro), with PEM thin film systems. The technique is simple, cheap, versatile and environmental friendly; as a consequence a variety of thin films can be easily fabricated. By proposing PEMs as non-mechanical and nanoscopic molecular closures, we aim to obtain hermetic sealing, good adhesive strength, and peel off ease. Atomic force microscopy (AFM) and colloidal probe techniques were used to characterize the morphology, roughness and adhesive properties of PEMs. AFM measurements were conducted in air, necessarily requiring careful control of ambient humidity. PEMs were formed by consecutive deposition of polyanions and polycations on a charged polyethylene terephthalate (PET) solid surface, the result of which was stable nanostructured films. By systemically varying the parameters of PEM build-up process: different combinations of polyelectrolytes, different numbers of bilayers (polyanion/polycation pairs), and miscellaneous types and concentrations of salts (NaCl, NaBr and NaF salts at 0.5 M and 1.0 M concentrations), the adhesion and morphology of PEMs were thoroughly investigated. The PEM thin films specifically investigated include poly(ethyleneimine) (PEI), poly(styrene sulfonate) (PSS), poly(allylamine hydrochloride) (PAH), poly(acrylic acid) (PAA), and poly(diallydimethylammonium chloride) (PDADMAC). Silica colloidal probes were utilized in the investigation, some of which were functionalized with COOH and/or coated with PEI-PSS. Silica colloidal probes were used in order to quantify interaction forces on the PEMs. A functionalized silica colloidal probe (a probe with COOH surface chemistry) and a silica colloidal probe coated with PEI-PSS were used to simulate PEM-PEM interactions. The results suggest that adhesion in the PEMs depend on the number of layers, the salt concentration and the salt type used during the build-up process, the environmental conditions where the adhesion force measurements were made, and the choice of probe. "

Studying the interactions between bacteria and soil colloidal particles in the environment is important for bioaugmentation purposes. Different factors affect the transport of the bacteria in porous media. For example, the soil type, the ionic strength of the substrate, and biological properties, such as the bacterial cell motility. Since organic materials are present in almost all subsurface media, the presence of natural organic matter (NOM) is considered an important factor influencing bacterial transport in porous media. In this work, a model system was developed to examine the interactions between natural colloidal particles and environmental bacteria using Atomic Force Microscopy (AFM). The natural colloids in the environment were modeled by a surface film of adsorbed NOM onto spherical SiO2 particles. Poly(methacrylic acid) (PMA), a simple linear polyelectrolyte, was used to mimic NOM since both are dominated by carboxylic acid functional groups. Soil Humic Acid (SHA) and Suwannee River Humic Acid (SRHA), two acidic polyelectrolytes, were used in further experiments to represent more complicated NOM. A smooth strain of Pseudomonas aeruginosa (PAO1) that coexpresses A-band and B-band polysaccharides, and its rough mutant (AK1401) that only expresses the A-band polysaccharides, were chosen to represent environmental bacteria. The model system was characterized through analysis of the measured forces between the chemically-modified colloidal probes and the bacterial cells. Interestingly, we found that PMA was not a good model for the more complex NOM substances. Differences were also observed in how each bacterium interacted with the three forms of NOM. For example, P. aeruginosa PAO1 had the highest adhesion with both complex forms of NOM, while P. aeruginosa AK1401 had the lowest adhesion with the complex forms of NOM. Since the lipopolysaccharide (LPS) structure is the only difference between the two strains, we attribute the different interactions to differences in LPS structure. The polymer density on the bacterial surface was found to be the most important factor in controlling the nature of the interaction forces.

The goal of this research was to develop a novel biosensor for detecting and eliminating pathogenic E. coli. Traditionally, identifying pathogenic E. coli and distinguishing it from harmless environmental strains includes serotyping and DNA sequencing, which can take days or weeks. Our biosensor platform makes use of a material that is part of the immune system from single- multi- cellular organisms that target viruses, fungi, and bacteria called antimicrobial peptides (AMPs). Using the quartz crystal microbalance with dissipation monitoring (QCM-D), we characterized non-specific binding between CP1 to silicon nitride and gold, and covalent binding of cysteine-terminated CP1 (CP1-cys) to gold. QCM-D monitors frequency and dissipative changes resulting from adsorbed mass, and peptide film thickness and density can be calculated using Voigt Viscoelastic modeling. Viability of the E. coli was monitored using a live/dead kit consisting of nucleic acid stains Syto 9 and Propidium Iodide. Successfully immobilizing peptide to a substrate is particularly important if CP1 would be applied on a food processing surface. By immobilizing CP1 to silicon nitride, we measured the binding forces between bacteria and peptides with the atomic force microscope (AFM), and explored important bacterial features such as LPS composition and length that influence binding affinity with CP1. The structure of the LPS is comprised of 3 sections: lipid A, core group, and O-antigen. We are mostly interested in the initial binding between AMP and LPS since our goal is to develop a novel biosensor that can detect pathogenic bacteria within seconds of exposure. Considering the short exposure period, the AMP would only be exposed to the O-antigen and outer core groups, which are repeating sugar chains that are essential for bacterial pathogenicity and adhesion to substrates. Although geared for use as a novel biosensor, results of this study can also be applied to the use of AMPs for replacing or enhancing the activity of antibiotics. Our work suggests that CP1 may not be serotype-specific, but targets the O-antigen before interfering with phospholipid groups of the bacterial membrane. Other factors that assist in pathogenicity, such as LPS length, may also be important for the consideration of CP1 potency.

The controlled organization of individual molecules and nanostructures with nanoscale accuracy is of great importance in the investigation of single-molecule events in biological and chemical assays, as well as for the fabrication of the next generation optoelectronic devices. In this regard, the precise patterning of individual molecules into hierarchical structures has attracted substantial research interest in recent years. DNA has been shown to be an ideal structural material for this purpose, due to the specificity of its programmability and outstanding chemical flexibility. DNA origami can display a high degree of positional and precise binding sites, allowing for complex arrangements and the assembly of different nanoscale architectures. In this project, we present a novel platform based on the use of DNA scaffolds for the organization of individual nanomoieties (with nanoscale spatial control), and their selective immobilisation on surfaces for single-molecule investigations. In particular, semiconductor quantum dots (QDs), fluorescence molecules, linear small peptides, and structural proteins were tethered with single-molecule accuracy on DNA origami; their subsequent organization in array configuration on nanopatterned surfaces allowed us to fabricate and test different platforms for single-molecule studies. In particular, we developed a Focused Ion Beam (FIB) nanofabrication strategy and demonstrated its general applicability for the assembly of functionalised DNA nanostructures in highly uniform nanoarrays, with single-molecule control. In addition, we further explored this nanofabricated platform for biological investigations at the single-molecule level, from protein-DNA interactions to cancer cell adhesion studies with single-molecule control. Investigations have been carried out via fluorescence microscopy, scanning electron microscopy (SEM), Focused Ion Beam (FIB) and atomic force microscopy (AFM). By and large, combining the programming ability of DNA as a scaffolding material with a one-step lithographic process, we have developed a platform of general applicability for the fabrication of nanoscale chips that can be employed in a variety of single-molecule investigations.