Photonic crystal waveguide (PCW) based device has been used in many applications in recent years due to its unique slow light effect. In this work, the application of PCW on sensing is presented. First, we present a PCW structure based Infrared (IR) spectroscopy combining with slot structure which has a large electric field enhancement for light-matter interaction for chemical sensing. The slow light effect and the electric field enhancement of our designed structure greatly enhance the absorption factor of chemical analytes by 1000. We then use multimode interference (MMI) optical splitter and Y junction combiner to connect two PCWs to show multiplexed detections of two chemicals on a single chip. Our results show the detection is down to 1 ppb for xylene in water and 100ppm for methane in nitrogen. We also present PCW microcavities structure for biological sensing in our work. Due to its high quality factor and easier immobilization of biomaterials, we are able to use ink jet printing method to bind the biomaterials on top of our chip. We choose linear-type 13 (L13, missing 13 holes) microcavities to do the biosensing for antibodies and cancer cell lysates because of its higher sensitivity combining with slow light effect. Our work achieves the cancer cell lysates detection down to 2 cells/μl., and further applications will be presented in our group in the future. / text

<p>FRET between pairs of fluorophores is widely used as a biological assay. However, the properties of larger fluorophore networks are poorly understood and their application space has not yet been fully explored. This dissertation introduces DNA self-assembled FÖrster Resonance Energy Transfer (FRET) networks that provide a unique optical output when probed by a series of light pulses. We create a Markov model of the FRET networks and analyze over 1200 time-resolved fluorescence measurements on 300 prototypical networks. Our results show that the optical responses of FRET networks are highly repeatable and minor variations between the FRET networks can be discriminated resulting in a total of 10375 unique responses. These results are used in the following breakthrough applications:</p><p>1. Unclonable Cryptographic Key for Secure Authentication and Communication</p><p>Modern authentication protocols rely on an asymmetry in the effort required by a legitimate user and an adversary to accurately decrypt an encoded message. These protocols ensure that communication between legitimate users is possible in polynomial time using a private key but a user without access to the exact key cannot compute the function using a probabilistic polynomial-time algorithm. Private-key cryptographic techniques currently employ physical keys based on algorithmic one-way functions, which are conjectured mathematical objects that are easy to compute but difficult to invert. Well-known examples of such one-way functions include the RSA and the Rabin functions. Although algorithmic one-way functions are widely used for authentication, their reliance on computational difficulty to provide security implies that they are not protected against future advances in computational capacity or speed. Also, use of a highly parallel network of conventional computers could potentially reverse engineer a key from the challenge-response pairs used in past communications. The key may also be obtained by duplicating the device. Most of the current physical embodiments of algorithmic one-way functions come with a tamper resistant packaging but remain vulnerable to sophisticated attacks.</p><p>We develop a RET based physical key to overcome the limitations of conventional security keys. The key exploits resonance energy transfer between a network of fluorophores placed on a nanostructure. The fluorophores provide a unique, unpredictable output when probed by a series of light pulses of specific wavelengths and delays. A critical advantage of the RET key over existing keys is that the manufacturing process allows two identical devices to be produced allowing us to exploit the advantages of symmetric key encryption, for the first time, without the need to physically transfer the device between the two communicating parties.</p><p>It is infeasible to model, characterize or replicate our key using modern cryptographic attacks including unfettered physical access to the device. This is because of the difficulty in characterizing the nanoscale structure and the large number of challenge-response pairs achievable for each key. Atomic force microscopy and time -resolved fluorescence measurements are performed to characterize the nanoscale structures. From over 1200 measurements on 300 prototypical keys, we estimate that a legitimate user would have a computational advantage of 10340 years over an attacker even if the attacker uses all the computational resources available in the world. Thus, the computational advantage of our key ensures perfect theoretical security for the foreseeable future. We provide an authentication protocol for use of the key and demonstrate that legitimate users are successfully authenticated 99.48% of the time with two trials. </p><p>2. Multiplexed Fluorescence Sensor for Cancer Detection</p><p>Fluorescence microscopy is one of the most widely used assays in biological systems. However, the technique suffers from limited multiplexing capability with previous attempts at detecting more than 11 fluorophores simultaneously resulting in barcodes that are too big for in vivo analysis, expensive and involve time-consuming detection schemes. Here, we introduce DNA self-assembled FRET networks that provide a unique, optical output when probed by a series of light pulses. Markov and entropy modeling of the nanoscale FRET sensors show that 125 fluorophores can be observed simultaneously. Furthermore, experimental analyses of over 1200 time-resolved fluorescence signatures show that the optical responses are repeatable 99.48% of the time and that minor variations between FRET networks can be discriminated resulting in a total of 10375 unique responses. This enormous increase in spatial information density enabled by FRET networks allowed us to identify molecular signatures in lung and breast cancer tumors.</p><p>It is now known that the presence of aberrant DNA/RNA secondary structure in the regulatory regions of genes involved in cell proliferation, cells growth and apoptosis can lead to cancer. The FRET sensor we designed, self-assembles DNA probes labeled with acceptor fluorophores to the target DNA/RNA secondary structure forming an optical network. A DNA strand labeled with a donor fluorophore triplex binds to a unique sequence adjacent to the secondary structure. When the donor fluorophore is excited, the optical network results in a different optical signal based on the presence of the wild-type or the aberrant secondary structure, through which we identified lung and breast cancer cells with high specificity and over 99.9% repeatability. The small size of fluorophores results in molecular scale spatial resolution while the optical sensing mechanism enables in vitro and in vivo characterization of the structure at picosecond resolution.</p> / Dissertation

L'objectif de ce travail de recherche est la réalisation de dispositifs à base de nanofils de silicium, réalisés par la méthode des espaceurs. La synthèse des nanofils est effectuée à partir d'une couche de silicium polycristallin, déposée par la technique LPCVD (Low Pressure Chemical Vapor Deposition). Ces nanofils sont ensuite intégrés dans les dispositifs électroniques tels que des résistances ou des transistors réalisés suivant deux configurations différentes « bottom-gate » et « step-gate ». Les caractéristiques électriques de ces deux types de transistors ont mis en évidence des propriétés électriques suffisantes pour leur utilisation en tant que capteurs. Une simulation permet d'expliquer l'effet de l'apport de charges électriques à la surface des nanofils sur la concentration d'électrons dans la couche active. Les dispositifs sont tout d'abord utilisés pour la mesure du pH, et montrent une sensibilité de détection supérieure à la sensibilité nernstienne. Pour une utilisation du dispositif en tant que biocapteur, une fonctionnalisation de la surface des nanofils est nécessaire pour permettre l'accrochage de sondes d'ADN. La détection électronique de l'hybridation sondes/cibles de brins d'ADN complémentaires est démontrée avec un faible seuil de détection. Enfin, afin d'augmenter la surface d'échange entre le nanofil et les espèces chargées, un procédé de fabrication de résistances à base de nanofils suspendus est développé. Des tests de détection en présence d'ammoniac ont mis en évidence une réponse linéaire sur une gamme de concentrations. Les résistances à base de nanofils suspendus présentent une plus grande sensibilité que celles à base de nanofils non suspendus, mettant en avant l'effet important de la surface des nanofils. Tous ces résultats permettent de démontrer la faisabilité de capteurs chimiques et biologiques à base de nanofils de silicium à partir des techniques conventionnelles de la microélectronique en utilisant un procédé de fabrication « bas-coût ». / The goal of this research work is the realization of devices based on silicon nanowires, realized using sidewall spacer formation technique. Nanowires are synthesized form a polycrystalline silicon layer deposited by LPCVD technique (Low Pressure Chemical Vapor Deposition). These nanowires are then integrated into electronic devices such as resistors and transistors made using two different configurations “bottom-gate” and “step-gate”. The electrical characteristics of these two types of transistors have shown adequate electrical properties for their use as sensors. A simulation is made, to explain how additional electrical charges on the surface of the nanowires, affect the electron concentration inside the active layer. The devices are firstly used for the pH measurement, and have shown sensitivity higher than the Nernstian sensitivity detection. For a use as biosensor, nanowires are functionnalized to allow the binding of DNA probes. Electronic detection of hybridization complementary probe/target DNA strands is demonstrated with a low detection limit. Finally, in order to increase the exchange surface between the nanowires and charged species, resistors based on suspended nanowires were developed. Different tests were performed in the presence of ammonia and showed a linear response over a range of concentrations. Resistors based on suspended nanowires highlighted greater sensitivity than those based on unsuspended nanowires, bringing out the important effect of the surface of the nanowires. All these results demonstrate the feasibility of chemical and biological sensors based on silicon nanowires compatible with conventional microelectronics techniques using a low-cost process.

A system was developed to perform real-time biological threat agent (BTA) detection with a small autonomous unmanned aerial vehicle (UAV). Biological sensors just recently reached a level of miniaturization and sensitivity that made UAV integration a feasible task. A Surface Plasmon Resonance (SPR) biosensor was integrated for the first time into a small UAV platform, allowing the UAV platform to collect and then quantify the concentration of an aerosolized biological agent in real-time. A sensor operator ran the SPR unit through a groundstation laptop and was able to wirelessly view detection results in real time. An aerial sampling mechanism was also developed for use with the SPR sensor. The collection system utilized a custom impinger setup to collect and concentrate aerosolized particles. The particles were then relocated and pressurized for use with the SPR sensor. The sampling system was tested by flying the UAV through a ground based plume of water soluble dye. During a second flight test utilizing the onboard SPR sensor, a sucrose solution was autonomously aerosolized, collected, and then detected by the combined sampling and SPR sensor subsystems, validating the system\'s functionality. The real-time BTA detection system has paved the way for future work quantifying biological agents in the atmosphere and performing source localization procedures. / Master of Science

No description available.

Les nanofils de semiconducteurs, d’oxides métalliques ou encore les nanotubes de carbone suscitent beaucoup d’intérêt pour des applications en nanoélectronique, mais également pour le développement de nanocapteurs chimiques ou biologiques. Cet intérêt pour les capteurs est principalement motivé par les propriétés liées aux faibles dimensions radiales et aux forts ratios surface/volume de ces nano-objets qui les rendent extrêmement sensibles aux effets de surface, et par conséquent à leur environnement. Les variations de charges de surface des matériaux en fonction du milieu peuvent également être utilisées comme une voie pour l’auto-organisation de nano-objets. Ce travail s’inscrit dans cette perspective. La voie chimique explorée pour la localisation est compatible avec une intégration de nano-objets a posteriori sur une technologie CMOS silicium. Plus précisément, notre approche « Bottom Up » repose sur les variations de la charge de surface du SiO2 et du Si3N4 en fonction du pH de la solution. Après une revue de littérature sur les points de charge nulle (PZC) des différents isolants selon leurs techniques d’élaboration, nous avons étudié expérimentalement les propriétés de couches de SiO2 thermique et de Si3N4 (LPCVD). Les PZC de ces différents isolants ont été déterminés par des mesures d’impédance électrochimique réalisées sur des structures EIS et couplées avec des mesures d’angle de contact en fonction du pH. Une étude systématique en fonction du pH (1.5 à 4.5) a été réalisée et un protocole expérimental a pu être mis en place pour démontrer la localisation préférentiellement les nanofils de silicium sur Si3N4. Nous avons pu démontrer qu’une localisation quasi parfaite était possible pour un pH compris entre 3 et 3,25 conformément au modèle électrostatique proposé. Le procédé développé présente l’avantage d’être simple, reproductible et peu coûteux. Il utilise une chimie très classique à température ambiante pour localiser des nano-objets silicium sans présenter de risque pour les dispositifs CMOS des niveaux inférieurs. / Semiconductor and metal oxides nanowires as well as carbon nanotubes are attractive for Nano electronic applications but also for chemical or biological sensors. This interest is related to the properties of 1D nanostructures with very small diameters and with high surface / volume ratios. The main property of such nanostructures is the high electrostatic sensitivity to their environment. The related surface charge variations as function of the medium may also be used as a way for the nanostructure self-organization. This work has been developed with this perspective. The investigated chemical approach is compatible with a post-integration of nano-objects on silicon CMOS technologies. More precisely, our “Bottom Up” method uses the different surface charges on SiO2 and Si3N4 as a function of the solution pH. After a literature review focused on the Point of Zero Charge (PZC) for insulating materials depending on the fabrication techniques, we have studied experimentally thermal SiO2 and LPCVD Si3N4 layers grown or deposited on silicon. The PZC of our layers have been determined using electrochemical impedance measurements in a EIS configuration. These impedance measurements have been cross correlated with contact angle measurements as function of the solution’s pH. A systematic study as function of pH in the 1.5 – 4.5 range as been carried out and an experimental protocol has been found in order to demonstrate the preferential localization of silicon nanowires on Si3N4. From this study, it is found that a quasi-perfect localization is possible for a pH between 3 and 3.25 as expected from the proposed electrostatic model. Finally, the developed process is low-cost, simple and reproducible which presents important advantages. It uses a very classical chemistry at ambient temperature and allows the localization of silicon nano-objects without any risk for the CMOS devices of the front-end level.