Yes / Here we present an in-depth analysis of structural factors that modulate peptide-capped nanoparticle catalytic activity via optically driven structural reconfiguration of the biointerface present at the particle surface. Six different sets of peptide-capped Au nanoparticles were prepared, in which an azobenzene photoswitch was incorporated into one of two well-studied peptide sequences with known affinity for Au, each at one of three different positions: The N- or C-terminus, or mid-sequence. Changes in the photoswitch isomerization state induce a reversible structural change in the surface-bound peptide, which modulates the catalytic activity of the material. This control of reactivity is attributed to changes in the amount of accessible metallic surface area available to drive the reaction. This research specifically focuses on the effect of the peptide sequence and photoswitch position in the biomolecule, from which potential target systems for on/off reactivity have been identified. Additionally, trends associated with photoswitch position for a peptide sequence (Pd4) have been identified. Integrating the azobenzene at the N-terminus or central region results in nanocatalysts with greater reactivity in the trans and cis conformations, respectively; however, positioning the photoswitch at the C-terminus gives rise to a unique system that is reactive in the trans conformation and partially deactivated in the cis conformation. These results provide a fundamental basis for new directions in nanoparticle catalyst development to control activity in real time, which could have significant implications in the design of catalysts for multistep reactions using a single catalyst. Additionally, such a fine level of interfacial structural control could prove to be important for applications beyond catalysis, including biosensing, photonics, and energy technologies that are highly dependent on particle surface structures. / Air Office of Scientific Research, grant number FA9550-12- 1-0226.

Cette thèse porte sur l'élaboration d'un biocapteur, à bas coût, pour la détection de pathogènes dans les secteurs de l'agroalimentaire et de l'environnement. Le modèle visé est la bactérie Escherichia coli, dont les souches pathogènes sont responsables, chaque année, de plusieurs crises sanitaires. L'utilisation de biocapteurs pour une détection rapide, sensible et sélective de pathogènes répond ainsi aux inquiétudes quant aux risques d'infection pour la population. Le capteur est constitué d'une fine membrane en arsénieure de gallium (GaAs) vibrant sur des modes de cisaillement d'épaisseur générés par champ électrique latéral via ses propriétés piézoélectriques. Nous montrons dans ce travail que la GaAs offre des possibilités de microfabrication, de biofonctionnalisation et de régénération intéressantes pour la conception d'un dispositif à bas coût. Nous avons mis en parallèle deux méthodes d'usinage de membranes minces : par voie chimique et par plasma, avec pour objectif, l'obtention de structures planes et lisse. Nous nous sommes intéressés à la réalisation d'une interface de bioreconnaissance. La caractérisation de celle-ci, par les techniques de spectroscope infrarouge à transformée de Fourier, nous a fait progresser sur a compréhension du phénomène d'auto-assemblage de molécules sur GaAs et nous a permis de développer des interfaces à haute densité. Nous avons étudié sa régénération et la photo-oxydation par UV a démontré un fort potentiel pour des applications de capteurs réutilisables. Enfin à travers des caractérisations électriques du transducteur, nous avons mis en avant l'impact de différents paramètres de l'environnement sur la réponse du dispositif. / This thesis addresses the development of a potentially low cost sensor dedicated for detection of pathogens in food industry processing and environment sectors. Such a sensor could serve detection of Escherichia coli bacteria whose pathogenic strains are the source of foodborne illnesses encountered worldwide every year. Hence, biosensor devices are needed for a rapid, sensitive and selective detection of pathogens to prevent outbreak risks. The design of the sensor consists of a resonant membrane fabricated in gallium arsenide (GaAs) crystal that operates at shear modes of bulk acoustic waves generated by lateral field excitation. In addition to its piezoelectric properties, as shown in this work, fabrication of a GaAs-based biosensor benefits from a well-developed technology of microfabrication and biofunctionalization and the possibility of regeneration that should result in cost savings of used devices. The transducer was fabricated by using typical clean room fabrication techniques. Plasma and wet etching were investigated and compared for achieving thin membranes with high quality surface morphology. Extensive research was carried out by Fourier transform infrared spectroscopy to determine optimum conditions for biofunctionalization of the GaAs surface. This activity allowed to advance the fundamental knowledge of self-assembly formation and, consequently, fabrication of high density biointerfaces. Among different biochip regeneration methods, it has been demonstrated that liquid UV photooxidation has a great potential for re-usable devices. Finally, operation of the transducer device was evaluated in various medium, simulating real conditions for detection.

Cette thèse s’inscrit dans le cadre d’une cotutelle internationale entre l’institut FEMTO-ST à Besançon en France et l’université de Sherbrooke au Canada. Elle porte sur l’élaboration d’un biocapteur, potentiellement à bas coût, pour la détection de pathogènes dans les secteurs de l’agroalimentaire, de l’environnement et de la biosécurité. Le modèle biologique visé est la bactérie Escherichia coli, dont les souches pathogènes sont responsables, chaque année et partout dans le monde, de plusieurs crises sanitaires liées à une mauvaise gestion des produits de consommation ou des installations de conditionnement ou de traitements de ces produits. L’utilisation de biocapteurs pour une détection rapide, sensible et sélective d’organismes pathogènes répond ainsi aux inquiétudes quant aux risques d’infection pour la population. La structure du capteur consiste en une fine membrane en arséniure de gallium (GaAs) vibrant sur des modes de cisaillement d’épaisseur générés par champ électrique latéral via les propriétés piézoélectriques du matériau. Nous montrons dans ce travail que le biocapteur offre également des possibilités de microfabrication, de biofonctionnalisation et de régénération intéressantes pour la conception d’un dispositif à bas coût. Le transducteur a été réalisé via des technologies de microfabrication utilisées en salle blanche avec une mise en parallèle des méthodes d’usinage par voie chimique et par plasma, l’objectif étant d’obtenir des membranes minces, planes et avec un état de surface de haute qualité. Une interface fluidique a été mise au point de façon à approvisionner de manière homogène le capteur en fluide. Par ailleurs, nos études se sont portées sur la fonctionnalisation biochimique de l’interface de bioreconnaissance sur l’arséniure de gallium et sa caractérisation fine par les techniques de spectroscopie infrarouge à transformée de Fourier (FTIR). Les résultats de cette étude ont permis de progresser sur la compréhension fondamentale du phénomène d’auto-assemblage de molécules sur GaAs. Un effort particulier a été mis en œuvre pour développer des biointerfaces de haute densité offrant une immobilisation optimale des immunorécepteurs biologiques. Parmi les différentes méthodes de régénération de la biointerface, le procédé de photo-oxydation UV en milieu liquide a démontré un fort potentiel pour des applications de capteurs réutilisables. Enfin, le transducteur a été caractérisé électriquement sous différents environnements. L’impact sur la réponse du résonateur des paramètres électriques, mécaniques et thermiques de ces milieux a été évalué afin de simuler le comportement du dispositif en condition réelle. / Abstract : This PhD thesis was realized in the context of a cotutelle program between FEMTO-ST institute in France and the University of Sherbrooke in Canada. The thesis addresses the development of a potentially low cost sensor dedicated for detection of pathogens in food industry processing, environment and biosafety sectors. Such a sensor could serve detection of Escherichia coli bacteria whose pathogenic strains are the source of foodborne illnesses encountered worldwide every year. Hence, biosensor devices are needed for a rapid, sensitive and selective detection of pathogens to avert, as soon as possible, any sources of contamination and prevent outbreak risks. The design of the sensor consists of a resonant membrane fabricated in gallium arsenide (GaAs) crystal that operates at shear modes of bulk acoustic waves generated by lateral field excitation. In addition to the attractive piezoelectric properties, as shown in this work, fabrication of a GaAs-based biosensor benefits from a well-developed technology of microfabrication of GaAs, as well as biofunctionalization and the possibility of regeneration that should result in cost savings of used devices. The transducer element was fabricated by using typical clean room microfabrication techniques. Plasma and wet etching were investigated and compared for achieving thin membranes with high quality surface morphology. At the same time, we designed and fabricated fluidic elements that allowed the construction of a flow cell chamber integrated in the sensor. Extensive research was carried out with a Fourier transform infrared spectroscopy (FTIR) diagnostic tool to determine optimum conditions for biofunctionalization of the GaAs surface. This activity allowed to advance the fundamental knowledge of self-assembly formation and, consequently, fabrication of high density biointerfaces for efficient immobilization of selected bioreceptors. Among different biochip regeneration methods, it has been demonstrated that liquid UV photooxidation (liquid-UVPO) has a great potential to deliver attractive surfaces for re-usable biochips. Finally, operation of the transducer device was evaluated in air environment and in various liquid media, simulating real conditions for detection.

This two-part thesis focuses on biointerfaces of two different biological systems. It specifically examines the interplay of structure and functionality in these biointerfaces. Part one studies photo-bio-electrochemically active bacteria and the strong dependence of their electrical current generation on electrode structure and pigment organisation. Part two uncovers surprising design principles of photonic structures on flower petals and presents research tools to study disordered optical systems. Biophotovoltaics (BPV) is a newly described biophysical effect in which a biofilm of photosynthetic microorganisms associated with an anode produces electrical current that can be harvested and passed through an external circuit. In this thesis-part, an experimental set-up is presented to quantitatively measure photo-electric activity of cyanobacteria in BPVs. Using this set-up, a systematic study of anode morphologies reveals that large electrode surface areas enhance photocurrents by two orders of magnitude, identifying structuration as key design criterion for bioelectrochemical interfaces. Electrodes with micrometer-sized pores allow enhanced direct contact area with bacteria, but with tested cyanobacteria this did not result in a photocurrent increase, disproving recent speculations in the literature. Furthermore, a theoretic-mathematical framework is presented to estimate light-energy utilisation in biofilms. It is detailed how pigment concentration and distribution affects the light-level dependent saturation of electron harvesting biofilms. This study brings the theory together with experiments, such as genetic modification and photo-current measurements. Part two of this thesis approaches the interaction of light and biointerface structuration from a different angle. In a significant extension of the candidate’s MPhil project, it was discovered that the disorder in natural photonic structures can be an advantage rather than a limitation in biology. With biological image analysis, optics simulations and nano-manufacturing a new photonic effect is uncovered which is iridescent but surprisingly constant in chroma. In collaboration with plant scientists, it is shown that many flowers have co-evolved disordered surface structuration that generates this bee visible colouration.

Adhesive processes in aqueous media play a crucial role in nature and are important for many technological processes. However, direct quantification of adhesion still requires expensive instrumentation while their sample throughput is rather small. Here we present a fast, and easily applicable method on quantifying adhesion energy in water based on interferometric measurement of polymer microgel contact areas with functionalized glass slides and evaluation via the Johnson–Kendall–Roberts (JKR) model. The advantage of the method is that the microgel matrix can be easily adapted to reconstruct various biological or technological adhesion processes. Here we study the suitability of the new adhesion method with two relevant examples: (1) antibody detection and (2) soil release polymers. The measurement of adhesion energy provides direct insights on the presence of antibodies showing that the method can be generally used for biomolecule detection. As a relevant example of adhesion in technology, the antiadhesive properties of soil release polymers used in today’s laundry products are investigated. Here the measurement of adhesion energy provides direct insights into the relation between polymer composition and soil release activity. Overall, the work shows that polymer hydrogel particles can be used as versatile adhesion sensors to investigate a broad range of adhesion processes in aqueous media.